Enrichment analysis
Priyadarshini Kachroo
11/29/2021
# restart R session
#.rs.restartR()
rm(list=ls())
system("hostname")
print(Sys.Date())## [1] "2021-11-29"print(Sys.time())## [1] "2021-11-29 20:21:40 EST"libs <- c("limma", "minfi", "ggpubr", "DMRcate", "gProfileR", "gplots", "QQperm", "DOSE", "enrichplot", "clusterProfiler", "org.Hs.eg.db", "R.utils", "knitr", "gprofiler2","ggpubr","gridExtra", "grid", "ggplot2", "lattice", "ggnewscale", "magrittr", "msigdbr")
for (l in libs) {
if (require(l, character.only = T)) {
print(paste0(l, " loaded successfully"))
} else {
install.packages(l)
require(l, character.only = T)
print(paste0(l, " installed and loaded successfully"))
}
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## If you use DOSE in published research, please cite:
## Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609## [1] "DOSE loaded successfully"## Loading required package: enrichplot##
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## If you use clusterProfiler in published research, please cite:
## Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.##
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timeStamp <- as.character(round(unclass(Sys.time())))
print(timeStamp)## [1] "1638235354"sig_digits <- 2
sum_sd <- function(data, varname) {
eval(parse(text = str_c("data[, round(summary(", varname, "), digits=2)] %>% print()")))
eval(parse(text = str_c("print(str_c('SD: ', data[, sd(", varname, ", na.rm = T) %>%
round(sig_digits)]))")))
}1. Data locations and loading
fhs.dir="/udd/reprk/projects/TOPMed/DNAm_data"
res.dir = "/proj/regeps/regep00/studies/CAMP/analyses/reprk/methylation/results/IgE_paper"
sub.plots.dir = file.path(res.dir, "plots")
merge_CG <- read.table(file=file.path(res.dir,
"CAMP_CRA_DMPs_fdr_logIgE_hg19_overlap_1630601015.txt"),
header=T,stringsAsFactors=F,sep='\t', quote="")
dim(merge_CG)## [1] 10426 62load(file=file.path(res.dir, "../norm.betas.camp_rcp_hg19_clean_allchr_1620830489.RData"))
norm.betas.rcp<-NULL;rm(norm.betas.rcp)
dim(ann850k)## [1] 865859 46merge_CG.all <- read.table(file=file.path(res.dir,
"CAMP_CRA_FHS_DMPs_fdr_logIgE_hg19_overlap_1630601015.txt"),
header=T,stringsAsFactors=F,sep='\t', quote="")
dim(merge_CG.all)## [1] 193 92# don't need to load FHS results for this, just the overlapping sites between all datasets as above
#fhs.fdr <- read.csv(file=file.path(fhs.dir,
# "IgE_offGen3_sample3471_adjSVp01_cellnoEOS_fdr5.csv"),
# as.is=TRUE, sep = ",", stringsAsFactors=FALSE)2. Data prep for enrichment analysis
# one of the issues could be that FHS is 450K and CRA/CAMP is 850K so for now I am using the 850K gene list of the platform as background. Ideally, I would have taken the overlap of genes annotated to the CpGs tested in all datasets under analysis as the background, but with different platforms, not sure about the best approach here
ann850k$Gene <- sub(";.*", "", ann850k$UCSC_RefGene_Name);
uniq.ge.plt <- unique(ann850k$Gene)
uniq.ge.plt <- uniq.ge.plt[uniq.ge.plt!="NA"]
uniq.ge.plt <- uniq.ge.plt[uniq.ge.plt!=""]
length(uniq.ge.plt)## [1] 26644head(uniq.ge.plt)## [1] "DDX11L1" "WASH5P" "OR4F5" "LOC101928626" "MIR1977"
## [6] "LOC100133331"write.table(uniq.ge.plt, file=file.path(res.dir,
paste0("uniq_background_genes_platform_", timeStamp, ".txt")),
sep="\t", quote=F, row.names=F)
uniq.hyper <- merge_CG[merge_CG$Direction_camp_cra=="++",]
uniq.hyper <- unique(uniq.hyper$Gene.x)
uniq.hyper <- uniq.hyper[uniq.hyper!="NA"]
uniq.hyper <- uniq.hyper[uniq.hyper!=""]
length(uniq.hyper)## [1] 1025write.table(uniq.hyper, file=file.path(res.dir,
paste0("cra_camp_uniq_hypermeth_genes_", timeStamp, ".txt")),
sep="\t", quote=F, row.names=F)
uniq.hypo <- merge_CG[merge_CG$Direction_camp_cra=="--",]
uniq.hypo <- unique(uniq.hypo$Gene.x)
uniq.hypo <- uniq.hypo[uniq.hypo!="NA"]
uniq.hypo <- uniq.hypo[uniq.hypo!=""]
length(uniq.hypo)## [1] 3520write.table(uniq.hypo, file=file.path(res.dir,
paste0("cra_camp_uniq_hypometh_genes_", timeStamp, ".txt")),
sep="\t", quote=F, row.names=F)3. enrichment gprofiler2 for CRA and CAMP
enrich.hyper <- gprofiler2::gost(query=uniq.hyper, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))## Detected custom background input, domain scope is set to 'custom'names(enrich.hyper)## [1] "result" "meta"# Results containing all annotated terms for hyper-methylated CpGs
gem <- enrich.hyper$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
head(gem); dim(gem)## GO.ID Description term_size intersection_size Domain
## 1497 MIRNA:000000 MIRNA root 14165 749 MIRNA
## 747 GO:0003674 molecular_function 17356 844 GO:MF
## 748 GO:0005515 protein binding 13924 726 GO:MF
## 749 GO:0005488 binding 15946 794 GO:MF
## 586 GO:0005737 cytoplasm 11268 618 GO:CC
## 587 GO:0005575 cellular_component 17335 831 GO:CC
## FDR Phenotype
## 1497 9.523048e-32 +1
## 747 4.230697e-29 +1
## 748 1.889285e-26 +1
## 749 2.472457e-26 +1
## 586 1.431912e-23 +1
## 587 1.431912e-23 +1
## Genes
## 1497 ZMIZ1,TGFBR2,C20orf27,GSG1,KIF5C,TREM2,XYLT1,ABL1,SLC7A7,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,LRRC27,UCK2,VAV2,DAAM1,KIF13B,MPO,ASB1,PCGF3,LPP,MGAT5,CAMKK2,KIAA1549L,DHX57,POC1B,DTNB,FAM180B,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,CUEDC1,FBN2,CAMK2G,PSMF1,NLRC4,LYPD4,CHST11,TERF2,PREX1,MDC1,NDUFS2,SLX4IP,POLE,SORCS2,WDFY4,DENND2D,VDR,FIG4,ASGR1,TOR3A,TRIM67,LIPC,SSH1,FOXK1,ITPKC,MACROD1,WDFY1,IRF5,SVIL,PRKCH,PSMB7,GM2A,INTS6,SSH2,VPS13B,FAM193B,ZDHHC14,CD244,SH3PXD2B,PPM1H,RNF44,SLC36A1,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,TNS1,TTC7B,IFFO2,KLHL25,GAS7,GALNT14,CDCP1,CLEC5A,GLIPR2,OPRM1,NEDD9,ZFR,MKNK1,CACNA2D2,NISCH,SFMBT2,CAMK1D,RBSN,CD82,SSBP3,EPB41L3,ARG1,CPM,NKG7,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,PCYOX1,ANKRD11,ACACA,ARHGEF10,ME3,SYNPO2,HSD17B12,ADAM19,KIDINS220,CYB561D1,PPM1F,RHBDF2,CUX1,ARSG,SPARC,KIAA0586,DYM,TNF,RPTOR,CCDC149,PECR,FKBP5,MTAP,AFF4,LARP1,BAZ1B,LIPA,UBN1,PML,NSMCE2,PXYLP1,ASAP2,B4GALNT3,SMG6,OTUB2,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,TMC7,IRAK2,FKBP9,OSBPL5,HOGA1,DEFA4,GPX3,HLX,MVP,PPP2R5C,EFR3B,DAGLB,TNS3,GDI2,COX10,AUH,MAST4,FTO,SCRIB,RBM20,MTMR7,FAM168A,SFXN5,ARL5C,AFAP1,SLC25A37,KCTD10,LRP3,SH3BP2,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,TRPM2,PCK2,ACSL6,SIRPA,PCOLCE2,FKBP15,SYNJ2,GATAD2A,ABCA13,ALDH2,ZNF791,CCRL2,WDR25,NAE1,ITPR1,UBASH3B,BTN2A2,IL18RAP,MED29,CRYL1,RCVRN,MIF4GD,LYN,SIRPG,TGOLN2,PIK3C2B,EPHB3,PROSER2,VTI1A,DLEU1,LCN2,UBXN2A,LASP1,ITPR2,RADIL,HIPK3,KIF21B,PCSK6,HRH1,KIAA0513,ETV6,SEPT9,PRPF6,FRMD4A,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,ADCY9,LITAF,RHOBTB2,SAG,TNFRSF1B,NAV3,TFDP1,NCKAP5L,NR3C1,VIT,PXN,SDCCAG8,AP1G1,MYOF,NID1,POR,SESTD1,SULT1B1,MAML2,WDR20,RAB11FIP1,FNDC3A,CISD3,INVS,OLA1,FHIT,FAM227B,DISC1,GAPVD1,MORC3,PEMT,CCDC102A,LAPTM4A,TAOK3,RIN2,SYNPO,GALNT2,MYH9,RGL1,PLEKHM3,KDM5B,AKAP13,LMTK2,OXR1,RFX3,LINGO1,CD300LG,BCL11A,GPR55,XXYLT1,SLC24A4,EPHA2,LARS2,CUL4A,RAPGEF2,LAMA3,TBC1D2B,TACC3,RGCC,USP10,SNAPC5,PRKCE,ZBTB20,CDHR2,CHST15,MCF2L2,SLC25A18,ART5,SEMA4C,GSG1L,ASPH,HCN4,NXPE3,MERTK,TSHZ3,SERPINA1,PSAP,SBF2,TMC8,ADAMTS8,ANTXR1,GGT6,ITGA5,AKAP2,C20orf144,B4GALT5,STOX2,TNFRSF11A,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,SLC43A2,ATP2B4,SLC38A1,UST,NFYC,S100A12,BLM,RBM47,RFTN2,HIVEP1,HEBP2,DENND3,SLC16A10,MYADM,AGRP,FAM53B,ZNF827,RAB40C,ECE1,KCNC4,INHBE,SLAIN1,LHFPL2,SAP30BP,TBC1D14,ZCCHC24,PIGR,INPP5D,IL6R,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,PKD1L1,SPRYD4,SURF6,RERE,VNN2,ERAP1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,TK2,CHCHD5,SLC11A1,UNC5B,SERTAD2,TRIO,TMC6,TNFRSF9,KIAA0825,SAMD4A,S100A9,FAM13A,AP1B1,GFI1,C16orf74,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,SLC2A9,RGS14,CYTH3,DCAF4L1,RAB5C,PLXND1,ITGA9,NOL4L,TCF3,ITPKB,TMEM105,SNX10,UBAC2,SLC39A10,HS3ST3B1,DNAL4,HMGCL,CTSD,TREM1,PRMT5,TMEM63A,IL27,TBXAS1,IL1R1,ADARB1,NAV2,GPLD1,ERGIC1,UXS1,LY6H,SDC2,SLC45A4,PRR5L,STK24,TMEM182,SYN3,SUSD6,CSF1,TRAF1,RAD54L2,PLCB1,RAD9B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,DEDD2,TRAK1,OTUB1,SETD2,PASK,PRR3,S100A8,PRDM2,RAB11FIP3,ABCB11,ELL2,KCTD4,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,BDH1,ZNF516,ECM2,PI4K2A,LPIN2,KIAA0195,HSPG2,AP3S2,HIVEP3,SLC39A11,HTR3A,ARFIP1,CRAT,PREP,RPS6KA2,PLXNB2,ARAP2,EP400,ANXA6,OGG1,MTF1,SLC26A9,BECN1,SLC19A1,IL18,UGCG,SPIDR,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,PGS1,SCARF1,MIER2,GOLIM4,NLN,TMCO3,RAP1GAP2,MBOAT2,TMEM72,SWAP70,TIAM1,PANX1,LDLRAD4,RAPGEF1,ROGDI,BIRC6,KDM4B,MAPKAPK2,PIM3,DUSP16,RASA3,PRKCD,ZSWIM7,FOXN3,DSTYK,POU2F3,ABCD4,CECR2,AADACL3,SBNO2,ZBTB47,RNF40,HSPA4L,NQO2,MGLL,NANOG,PDE4B,MYO1F,AATK,CMTM2,VPS53,INPP4A,NFAM1,USP36,PEX5,ANG,MED26,GSN,NOS1AP,GDPD5,LGR4,BTD,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,ARID3B,TOM1L2,CCDC69,XRCC5,ABCA3,DOCK10,DPYSL3,RFX1,CPEB4,RASAL2,BLCAP,LMO7,CHI3L2,JDP2,CERS6,ACTN1,BACE1,MAP2K6,GARNL3,CPAMD8,PAG1,GAS8,FEZ2,WDFY3,ENO1,SPRED2,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,SDHAF3,ZNF319,CYB561,SENP5,NNMT,NOD2,STX1B,GRAP2,KDM7A,GJB6,MICALCL,KCNMB1,TMEM2,AJUBA,EIF4G1,SORL1,IL18BP,TJAP1,VAC14,GXYLT2,SULF2,MYO5A,ZMYND11,C16orf70,FAM126A,CCDC30,ADRA1A,TSPAN18,GTDC1,FNDC3B,CALML4,DLC1,GJA8,SORCS3,CCDC92,DENND1A,TCEA1,FCHSD2,HEYL,ST6GAL1,BTBD19,SFT2D1,MAST3,CDC42BPB,DNMT3A,CTSH,TSPAN3,PPM1M,PRPSAP1,HAVCR2,IQCG,CTNNBIP1,ANKRD33B,PDGFD,SLC37A2,NDUFA10,STXBP2,ATP11B,ZBTB17,BCAS4,CYSTM1,CCDC88C,KAT6B,DCUN1D2,NEK6,NYNRIN,MARK3,FGD4,BCL2L15,PLXNC1,FLYWCH1,MACF1,SF3B3,DOT1L,KCNJ15,GPATCH2,RGS3,AVPI1,LMF1,TM9SF4,RBM33,SLCO2A1,KIAA1549,RAB31,ADK,SETD1A,CPNE6,MPRIP,WDHD1,CCDC34,ADPGK,TNIP3,SMAD1,GPRIN3,GPR161,TVP23A,RGS12,MFGE8,TBC1D22A,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,TBC1D1,RNF144A,SLC6A6,DGKI,ZNF398,SIK3,EPHA4,SLIT1,CACNA1C,HRC,POLA2,SV2C,EPB41,IFT140,PRRG4,WIPF3,MRPL1,LRP4,DIP2C,ABCC2,MBP,CACHD1,RNF216,USP47,PPP1R13B,SCYL2,AP3M2,ERI3,GABBR1,APBB1,USP25,FAM83D,SMARCA2,SLC22A4,KCNN3,FSTL4,ZDHHC24,NCLN,LRIG1,ZNF695,ANKS6,CXADR,TMEM30A,PPM1E,IFFO1,ROBO4,VAMP1
## 747 TFR2,ZMIZ1,TGFBR2,C20orf27,GSG1,RBKS,KIF5C,TREM2,XYLT1,ABL1,RUFY4,SLC7A7,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,LRRC27,FCER2,UCK2,AZU1,VAV2,DAAM1,KIF13B,MPO,TARM1,ASB1,PCGF3,LPP,MGAT5,CAMKK2,DHX57,POC1B,DTNB,FAM180B,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,CUEDC1,FBN2,CAMK2G,PSMF1,NLRC4,CHST11,TERF2,PREX1,SLC36A3,PRKAG2,MDC1,ABCA9,NDUFS2,SLX4IP,POLE,SORCS2,WDFY4,DENND2D,VDR,FIG4,ASGR1,TOR3A,TRIM67,LIPC,SSH1,IL19,FOXK1,ITPKC,MACROD1,WDFY1,IRF5,SVIL,TNN,PRKCH,PSMB7,GM2A,INTS6,SSH2,MOK,FAM193B,ZDHHC14,CD244,SH3PXD2B,PPM1H,LRRK1,RNF44,SLC36A1,CTSG,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,LPO,TNS1,TTC7B,KLHL25,GAS7,GALNT14,CDCP1,ACOXL,CLEC5A,GLIPR2,DLEU7,OPRM1,SLC10A1,NEDD9,ZFR,MKNK1,CACNA2D2,NISCH,SFMBT2,PTX4,CAMK1D,NGF,RBSN,CD82,SSBP3,EPB41L3,ARG1,CPM,NKG7,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,PCYOX1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,SYNPO2,HSD17B12,ADAM19,KIDINS220,CYB561D1,PPM1F,RHBDF2,CUX1,ARSG,SPARC,DYM,TNF,RPTOR,PECR,FKBP5,MTAP,AFF4,MEFV,LARP1,BAZ1B,LIPA,UBN1,PML,NSMCE2,PXYLP1,ASAP2,B4GALNT3,SMG6,OTUB2,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,TMC7,IRAK2,FKBP9,OSBPL5,HOGA1,DEFA4,GPX3,HLX,MVP,PPP2R5C,EFR3B,DAGLB,MIR145,TNS3,GDI2,COX10,AUH,MAST4,FTO,SCRIB,RBM20,MTMR7,ARRDC5,MARCO,FAM168A,SFXN5,FCN1,ARL5C,AFAP1,SLC25A37,KCTD10,LRP3,RGL4,SH3BP2,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,TRPM2,PCK2,ACSL6,SIRPA,PCOLCE2,FKBP15,SYNJ2,MEGF6,STX8,GATAD2A,ABCA13,ALDH2,ZNF791,CCRL2,WDR25,NAE1,ITPR1,UBASH3B,BTN2A2,IL18RAP,MED29,CRYL1,RCVRN,MIF4GD,LYN,SIRPG,TGOLN2,RETN,PIK3C2B,EPHB3,PROSER2,VTI1A,CREB3L4,LCN2,UBXN2A,LASP1,ITPR2,RADIL,HIPK3,KIF21B,PCSK6,HRH1,ETV6,SEPT9,MYCBPAP,PRPF6,GGT1,FRMD4A,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,ADCY9,LITAF,RHOBTB2,SAG,TNFRSF1B,KCNAB2,NAV3,UPB1,TFDP1,NCKAP5L,NR3C1,VIT,MCCC1,PXN,SDCCAG8,AP1G1,MYOF,GPR68,NID1,POR,SESTD1,SULT1B1,MAML2,WDR20,RAB11FIP1,FNDC3A,CISD3,INVS,OLA1,FHIT,DISC1,GAPVD1,MYL3,MORC3,TSKS,PEMT,CCDC102A,LAPTM4A,TAOK3,RIN2,SYNPO,SLC25A35,GALNT2,MYH9,RGL1,PRTN3,PLEKHM3,KDM5B,DYSF,AKAP13,LMTK2,SLAMF8,OXR1,RFX3,LINGO1,CD300LG,BCL11A,GPR55,XXYLT1,SLC24A4,EPHA2,LARS2,CUL4A,RAPGEF2,LAMA3,TBC1D2B,AP1G2,LIMK2,TACC3,PDE1C,SH3RF3,ITGAE,RGCC,USP10,SNAPC5,PRKCE,ZBTB20,CDHR2,CHST15,MCF2L2,PDZK1IP1,SLC25A18,ART5,TM4SF4,SEMA4C,GSG1L,ASPH,HCN4,NXPE3,MERTK,TSHZ3,SERPINA1,PSAP,SBF2,TMC8,ADAMTS8,ANTXR1,GGT6,KRT17,ITGA5,AKAP2,B4GALT5,STOX2,TNFRSF11A,STK39,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,SLC43A2,CCDC148,ATP2B4,SLC38A1,UST,CYP3A7-CYP3A51P,NFYC,IGFBP6,S100A12,PSEN2,BLM,IL16,RBM47,RFTN2,HIVEP1,HEBP2,DENND3,SLC16A10,MYADM,FGD5,AGRP,FAM53B,ZNF827,SRGAP3,RAB40C,ECE1,KCNC4,INHBE,SLAIN1,LHFPL2,SAP30BP,TBC1D14,ZCCHC24,PIGR,INPP5D,IL6R,DOCK2,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,PKD1L1,SPRYD4,CLDN15,SURF6,RERE,VNN2,ERAP1,CHIT1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,TK2,CHCHD5,SLC11A1,UNC5B,SERTAD2,TRIO,TMC6,FAP,TNFRSF9,KIAA0825,SAMD4A,S100A9,FAM13A,AP1B1,PHF11,GFI1,C16orf74,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,SLC2A9,RGS14,CYTH3,BTBD11,DCAF4L1,RAB5C,PLXND1,ITGA9,NOL4L,TCF3,ITPKB,SNX10,UBAC2,SLC39A10,HS3ST3B1,DNAL4,HMGCL,CTSD,TREM1,TESC,PRMT5,TMEM63A,SP140,IL27,TBXAS1,IL1R1,ADARB1,GIMAP1-GIMAP5,HHIPL2,NAV2,GPLD1,ERGIC1,UXS1,LY6H,SDC2,SLC45A4,PRR5L,STK24,TMEM182,SEMA4A,SYN3,SUSD6,CSF1,TRAF1,TSGA13,RAD54L2,PLCB1,RAD9B,SEC22B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,DEDD2,TRAK1,OTUB1,SETD2,PASK,PRR3,IDO2,S100A8,FERMT3,PRDM2,DPYS,RAB11FIP3,ABCB11,ELL2,KCTD4,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,BDH1,ZNF516,ECM2,PI4K2A,LPIN2,HSPG2,HIVEP3,SLC39A11,HTR3A,ARFIP1,CRAT,PREP,RPS6KA2,PLXNB2,ARAP2,EP400,ANXA6,OGG1,MTF1,SLC26A9,BECN1,SLC19A1,IL18,UGCG,SPIDR,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,PGS1,SCARF1,MIER2,NLN,TMCO3,RAPSN,RAP1GAP2,MBOAT2,TMEM72,SWAP70,TIAM1,PANX1,C11orf45,LDLRAD4,RAPGEF1,ROGDI,BIRC6,KDM4B,MAPKAPK2,UBE2L6,PIK3R5,PIM3,DUSP16,RASA3,CHI3L1,PRKCD,ZSWIM7,FOXN3,DSTYK,POU2F3,ABCD4,CECR2,AADACL3,SBNO2,ZBTB47,RNF40,RNASE11,HSPA4L,NQO2,CSF3,MGLL,GLIS1,NANOG,AK5,PDE4B,MYO1F,AATK,CMTM2,VPS53,INPP4A,NFAM1,USP36,FA2H,PEX5,ANG,MED26,GSN,NOS1AP,GDPD5,LGR4,BTD,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,FCHO1,ARID3B,TOM1L2,CCDC69,DRGX,XRCC5,ABCA3,DOCK10,DPYSL3,RFX1,CPEB4,RASAL2,BLCAP,LMO7,CHI3L2,JDP2,CERS6,ACTN1,BACE1,MAP2K6,GARNL3,CPAMD8,PAG1,GAS8,FEZ2,SH2B2,WDFY3,ENO1,SPRED2,FAM174A,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,RNASE9,ZNF319,CYB561,SENP5,NNMT,NOD2,STX1B,GRAP2,KDM7A,GJB6,MICALCL,KCNMB1,TMEM2,AJUBA,EIF4G1,SORL1,IL18BP,TJAP1,VAC14,GXYLT2,SULF2,MYO5A,ZMYND11,C16orf70,TEX12,FAM126A,ADRA1A,GTDC1,FNDC3B,CALML4,DLC1,GJA8,SORCS3,CCDC92,DENND1A,TCEA1,FCHSD2,HEYL,ST6GAL1,BTBD19,SFT2D1,CATIP,MAST3,CDC42BPB,DNMT3A,CTSH,TSPAN3,PPM1M,ZNF385C,PRPSAP1,OTUD6B,HAVCR2,IQCG,CTNNBIP1,ANKRD33B,PDGFD,SLC37A2,ARMC9,NDUFA10,STXBP2,ATP11B,ZBTB17,BCAS4,CYSTM1,CCDC88C,KAT6B,ELANE,DCUN1D2,NEK6,NYNRIN,MARK3,FGD4,BCL2L15,PLXNC1,FLYWCH1,MACF1,SF3B3,FHAD1,DOT1L,IL22RA2,KCNJ15,GPATCH2,RGS3,GLT1D1,AVPI1,TM9SF4,HLA-DMB,RBM33,SLCO2A1,RAB31,ADK,SETD1A,CPNE6,CPN1,MPRIP,WDHD1,CLCN1,CCDC34,ADPGK,TNIP3,SMAD1,GPR161,TVP23A,RGS12,MFGE8,TBC1D22A,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,TBC1D1,RNF144A,SLC6A6,DGKI,WDR49,SERPINB13,ZNF398,SIK3,EPHA4,SLIT1,CACNA1C,HRC,SLC22A11,POLA2,SV2C,PHACTR1,EPB41,IFT140,PRRG4,WIPF3,MRPL1,LRP4,DIP2C,ABCC2,MBP,ELOVL3,CACHD1,RNF216,USP47,PPP1R13B,ANO10,SCYL2,AP3M2,ERI3,ICA1,GABBR1,PPP1R1B,APBB1,CDH26,USP25,FAM83D,SMARCA2,SLC22A4,KCNN3,PPCDC,ERC2,FSTL4,ZDHHC24,NCLN,LRIG1,BPIFB1,ZNF695,ANKS6,CXADR,TMEM30A,PPM1E,IFFO1,ROBO4,VAMP1,STARD9
## 748 TFR2,ZMIZ1,TGFBR2,C20orf27,GSG1,RBKS,KIF5C,TREM2,ABL1,RUFY4,CARS,ATN1,NCOR2,GALNT6,COL23A1,LRRC27,FCER2,UCK2,AZU1,VAV2,DAAM1,KIF13B,MPO,TARM1,ASB1,PCGF3,LPP,CAMKK2,DHX57,POC1B,DTNB,FAM180B,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,CUEDC1,FBN2,CAMK2G,PSMF1,NLRC4,TERF2,PREX1,PRKAG2,MDC1,NDUFS2,SLX4IP,POLE,SORCS2,WDFY4,DENND2D,VDR,FIG4,ASGR1,TRIM67,LIPC,SSH1,IL19,FOXK1,ITPKC,MACROD1,WDFY1,IRF5,SVIL,TNN,PRKCH,PSMB7,INTS6,SSH2,FAM193B,CD244,SH3PXD2B,PPM1H,LRRK1,RNF44,SLC36A1,CTSG,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,TNS1,TTC7B,KLHL25,GAS7,CDCP1,GLIPR2,OPRM1,SLC10A1,NEDD9,ZFR,MKNK1,NISCH,SFMBT2,CAMK1D,NGF,RBSN,CD82,SSBP3,EPB41L3,ARG1,NKG7,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,PCYOX1,ZNF438,ANKRD11,ACACA,ARHGEF10,SYNPO2,HSD17B12,ADAM19,KIDINS220,CYB561D1,PPM1F,RHBDF2,SPARC,DYM,TNF,RPTOR,PECR,FKBP5,MTAP,AFF4,MEFV,LARP1,BAZ1B,UBN1,PML,NSMCE2,PXYLP1,ASAP2,SMG6,OTUB2,TPD52L2,ROPN1L,PCNT,RALGAPA2,IRAK2,HOGA1,DEFA4,GPX3,HLX,MVP,PPP2R5C,EFR3B,DAGLB,MIR145,TNS3,GDI2,MAST4,FTO,SCRIB,RBM20,MTMR7,ARRDC5,MARCO,FAM168A,SFXN5,FCN1,AFAP1,SLC25A37,KCTD10,LRP3,SH3BP2,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,PCK2,ACSL6,SIRPA,PCOLCE2,FKBP15,SYNJ2,MEGF6,STX8,GATAD2A,ZNF791,CCRL2,WDR25,NAE1,ITPR1,UBASH3B,BTN2A2,IL18RAP,MED29,CRYL1,MIF4GD,LYN,SIRPG,TGOLN2,RETN,PIK3C2B,EPHB3,PROSER2,VTI1A,CREB3L4,LCN2,UBXN2A,LASP1,ITPR2,RADIL,KIF21B,PCSK6,ETV6,SEPT9,MYCBPAP,PRPF6,GGT1,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,LITAF,RHOBTB2,SAG,TNFRSF1B,KCNAB2,NAV3,UPB1,TFDP1,NCKAP5L,NR3C1,MCCC1,PXN,SDCCAG8,AP1G1,MYOF,NID1,POR,SESTD1,SULT1B1,WDR20,RAB11FIP1,FNDC3A,INVS,OLA1,FHIT,DISC1,GAPVD1,MYL3,MORC3,TSKS,PEMT,LAPTM4A,TAOK3,SYNPO,SLC25A35,GALNT2,MYH9,RGL1,PRTN3,KDM5B,DYSF,AKAP13,LMTK2,SLAMF8,OXR1,RFX3,LINGO1,CD300LG,BCL11A,EPHA2,CUL4A,RAPGEF2,LAMA3,TBC1D2B,AP1G2,LIMK2,TACC3,PDE1C,SH3RF3,RGCC,USP10,SNAPC5,PRKCE,ZBTB20,CDHR2,CHST15,PDZK1IP1,SLC25A18,TM4SF4,SEMA4C,GSG1L,ASPH,HCN4,NXPE3,MERTK,TSHZ3,SERPINA1,PSAP,SBF2,TMC8,ADAMTS8,ANTXR1,GGT6,KRT17,ITGA5,AKAP2,TNFRSF11A,STK39,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,SLC43A2,CCDC148,ATP2B4,SLC38A1,NFYC,IGFBP6,S100A12,PSEN2,BLM,IL16,RBM47,RFTN2,HIVEP1,HEBP2,DENND3,SLC16A10,MYADM,FGD5,AGRP,FAM53B,ZNF827,SRGAP3,ECE1,KCNC4,INHBE,SLAIN1,LHFPL2,SAP30BP,TBC1D14,INPP5D,IL6R,DOCK2,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,PKD1L1,SPRYD4,CLDN15,SURF6,RERE,VNN2,ERAP1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,CHCHD5,SLC11A1,UNC5B,SERTAD2,TRIO,TMC6,FAP,TNFRSF9,KIAA0825,SAMD4A,S100A9,AP1B1,PHF11,GFI1,C16orf74,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,SLC2A9,RGS14,CYTH3,BTBD11,DCAF4L1,RAB5C,PLXND1,ITGA9,NOL4L,TCF3,ITPKB,SNX10,UBAC2,DNAL4,CTSD,TREM1,TESC,PRMT5,TMEM63A,SP140,IL27,IL1R1,ADARB1,HHIPL2,NAV2,ERGIC1,UXS1,LY6H,SDC2,PRR5L,STK24,TMEM182,SEMA4A,SUSD6,CSF1,TRAF1,TSGA13,RAD54L2,PLCB1,RAD9B,SEC22B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,DEDD2,TRAK1,OTUB1,SETD2,PASK,PRR3,S100A8,FERMT3,PRDM2,DPYS,RAB11FIP3,ABCB11,ELL2,KCTD4,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,ECM2,PI4K2A,HSPG2,HTR3A,ARFIP1,PREP,RPS6KA2,PLXNB2,ARAP2,EP400,ANXA6,OGG1,MTF1,SLC26A9,BECN1,SLC19A1,IL18,UGCG,SPIDR,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,SCARF1,MIER2,RAPSN,RAP1GAP2,TMEM72,SWAP70,TIAM1,PANX1,C11orf45,LDLRAD4,RAPGEF1,ROGDI,BIRC6,MAPKAPK2,UBE2L6,PIM3,DUSP16,CHI3L1,PRKCD,ZSWIM7,FOXN3,POU2F3,ABCD4,CECR2,SBNO2,ZBTB47,RNF40,RNASE11,NQO2,CSF3,MGLL,GLIS1,NANOG,PDE4B,MYO1F,AATK,CMTM2,VPS53,INPP4A,NFAM1,USP36,FA2H,PEX5,ANG,MED26,GSN,NOS1AP,GDPD5,LGR4,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,FCHO1,ARID3B,TOM1L2,CCDC69,XRCC5,DOCK10,DPYSL3,RFX1,CPEB4,RASAL2,BLCAP,LMO7,JDP2,CERS6,ACTN1,BACE1,MAP2K6,CPAMD8,PAG1,GAS8,FEZ2,SH2B2,WDFY3,ENO1,SPRED2,FAM174A,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,ZNF319,CYB561,SENP5,NOD2,STX1B,GRAP2,KDM7A,GJB6,MICALCL,KCNMB1,TMEM2,AJUBA,EIF4G1,SORL1,IL18BP,TJAP1,VAC14,MYO5A,ZMYND11,C16orf70,TEX12,FAM126A,ADRA1A,FNDC3B,DLC1,GJA8,SORCS3,CCDC92,DENND1A,TCEA1,FCHSD2,HEYL,ST6GAL1,BTBD19,SFT2D1,CATIP,MAST3,CDC42BPB,DNMT3A,CTSH,ZNF385C,PRPSAP1,HAVCR2,IQCG,CTNNBIP1,ANKRD33B,PDGFD,ARMC9,STXBP2,ATP11B,ZBTB17,BCAS4,CYSTM1,CCDC88C,KAT6B,ELANE,DCUN1D2,NEK6,MARK3,FGD4,BCL2L15,PLXNC1,FLYWCH1,MACF1,SF3B3,FHAD1,DOT1L,IL22RA2,KCNJ15,GPATCH2,RGS3,AVPI1,TM9SF4,HLA-DMB,SLCO2A1,RAB31,SETD1A,CPNE6,CPN1,MPRIP,WDHD1,CLCN1,CCDC34,TNIP3,SMAD1,GPR161,TVP23A,RGS12,MFGE8,TBC1D22A,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,TBC1D1,RNF144A,DGKI,WDR49,SERPINB13,ZNF398,SIK3,EPHA4,SLIT1,CACNA1C,HRC,SLC22A11,POLA2,SV2C,PHACTR1,EPB41,IFT140,PRRG4,WIPF3,MRPL1,LRP4,ABCC2,MBP,ELOVL3,RNF216,USP47,PPP1R13B,SCYL2,AP3M2,ICA1,GABBR1,PPP1R1B,APBB1,CDH26,USP25,FAM83D,SMARCA2,SLC22A4,KCNN3,PPCDC,ERC2,FSTL4,ZDHHC24,NCLN,LRIG1,ZNF695,ANKS6,CXADR,TMEM30A,PPM1E,IFFO1,ROBO4,VAMP1,STARD9
## 749 TFR2,ZMIZ1,TGFBR2,C20orf27,GSG1,RBKS,KIF5C,TREM2,XYLT1,ABL1,RUFY4,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,LRRC27,FCER2,UCK2,AZU1,VAV2,DAAM1,KIF13B,MPO,TARM1,ASB1,PCGF3,LPP,MGAT5,CAMKK2,DHX57,POC1B,DTNB,FAM180B,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,CUEDC1,FBN2,CAMK2G,PSMF1,NLRC4,TERF2,PREX1,PRKAG2,MDC1,ABCA9,NDUFS2,SLX4IP,POLE,SORCS2,WDFY4,DENND2D,VDR,FIG4,ASGR1,TOR3A,TRIM67,LIPC,SSH1,IL19,FOXK1,ITPKC,MACROD1,WDFY1,IRF5,SVIL,TNN,PRKCH,PSMB7,INTS6,SSH2,MOK,FAM193B,CD244,SH3PXD2B,PPM1H,LRRK1,RNF44,SLC36A1,CTSG,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,LPO,TNS1,TTC7B,KLHL25,GAS7,GALNT14,CDCP1,ACOXL,CLEC5A,GLIPR2,OPRM1,SLC10A1,NEDD9,ZFR,MKNK1,CACNA2D2,NISCH,SFMBT2,PTX4,CAMK1D,NGF,RBSN,CD82,SSBP3,EPB41L3,ARG1,CPM,NKG7,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,PCYOX1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,SYNPO2,HSD17B12,ADAM19,KIDINS220,CYB561D1,PPM1F,RHBDF2,CUX1,ARSG,SPARC,DYM,TNF,RPTOR,PECR,FKBP5,MTAP,AFF4,MEFV,LARP1,BAZ1B,UBN1,PML,NSMCE2,PXYLP1,ASAP2,SMG6,OTUB2,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,OSBPL5,HOGA1,DEFA4,GPX3,HLX,MVP,PPP2R5C,EFR3B,DAGLB,MIR145,TNS3,GDI2,AUH,MAST4,FTO,SCRIB,RBM20,MTMR7,ARRDC5,MARCO,FAM168A,SFXN5,FCN1,ARL5C,AFAP1,SLC25A37,KCTD10,LRP3,SH3BP2,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,TRPM2,PCK2,ACSL6,SIRPA,PCOLCE2,FKBP15,SYNJ2,MEGF6,STX8,GATAD2A,ABCA13,ALDH2,ZNF791,CCRL2,WDR25,NAE1,ITPR1,UBASH3B,BTN2A2,IL18RAP,MED29,CRYL1,RCVRN,MIF4GD,LYN,SIRPG,TGOLN2,RETN,PIK3C2B,EPHB3,PROSER2,VTI1A,CREB3L4,LCN2,UBXN2A,LASP1,ITPR2,RADIL,HIPK3,KIF21B,PCSK6,ETV6,SEPT9,MYCBPAP,PRPF6,GGT1,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,ADCY9,LITAF,RHOBTB2,SAG,TNFRSF1B,KCNAB2,NAV3,UPB1,TFDP1,NCKAP5L,NR3C1,VIT,MCCC1,PXN,SDCCAG8,AP1G1,MYOF,NID1,POR,SESTD1,SULT1B1,WDR20,RAB11FIP1,FNDC3A,CISD3,INVS,OLA1,FHIT,DISC1,GAPVD1,MYL3,MORC3,TSKS,PEMT,LAPTM4A,TAOK3,SYNPO,SLC25A35,GALNT2,MYH9,RGL1,PRTN3,PLEKHM3,KDM5B,DYSF,AKAP13,LMTK2,SLAMF8,OXR1,RFX3,LINGO1,CD300LG,BCL11A,XXYLT1,EPHA2,LARS2,CUL4A,RAPGEF2,LAMA3,TBC1D2B,AP1G2,LIMK2,TACC3,PDE1C,SH3RF3,ITGAE,RGCC,USP10,SNAPC5,PRKCE,ZBTB20,CDHR2,CHST15,PDZK1IP1,SLC25A18,TM4SF4,SEMA4C,GSG1L,ASPH,HCN4,NXPE3,MERTK,TSHZ3,SERPINA1,PSAP,SBF2,TMC8,ADAMTS8,ANTXR1,GGT6,KRT17,ITGA5,AKAP2,B4GALT5,TNFRSF11A,STK39,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,SLC43A2,CCDC148,ATP2B4,SLC38A1,CYP3A7-CYP3A51P,NFYC,IGFBP6,S100A12,PSEN2,BLM,IL16,RBM47,RFTN2,HIVEP1,HEBP2,DENND3,SLC16A10,MYADM,FGD5,AGRP,FAM53B,ZNF827,SRGAP3,RAB40C,ECE1,KCNC4,INHBE,SLAIN1,LHFPL2,SAP30BP,TBC1D14,ZCCHC24,INPP5D,IL6R,DOCK2,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,PKD1L1,SPRYD4,CLDN15,SURF6,RERE,VNN2,ERAP1,CHIT1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,TK2,CHCHD5,SLC11A1,UNC5B,SERTAD2,TRIO,TMC6,FAP,TNFRSF9,KIAA0825,SAMD4A,S100A9,AP1B1,PHF11,GFI1,C16orf74,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,SLC2A9,RGS14,CYTH3,BTBD11,DCAF4L1,RAB5C,PLXND1,ITGA9,NOL4L,TCF3,ITPKB,SNX10,UBAC2,DNAL4,HMGCL,CTSD,TREM1,TESC,PRMT5,TMEM63A,SP140,IL27,TBXAS1,IL1R1,ADARB1,GIMAP1-GIMAP5,HHIPL2,NAV2,ERGIC1,UXS1,LY6H,SDC2,PRR5L,STK24,TMEM182,SEMA4A,SYN3,SUSD6,CSF1,TRAF1,TSGA13,RAD54L2,PLCB1,RAD9B,SEC22B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,DEDD2,TRAK1,OTUB1,SETD2,PASK,PRR3,IDO2,S100A8,FERMT3,PRDM2,DPYS,RAB11FIP3,ABCB11,ELL2,KCTD4,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,ZNF516,ECM2,PI4K2A,HSPG2,HIVEP3,HTR3A,ARFIP1,PREP,RPS6KA2,PLXNB2,ARAP2,EP400,ANXA6,OGG1,MTF1,SLC26A9,BECN1,SLC19A1,IL18,UGCG,SPIDR,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,PGS1,SCARF1,MIER2,NLN,RAPSN,RAP1GAP2,TMEM72,SWAP70,TIAM1,PANX1,C11orf45,LDLRAD4,RAPGEF1,ROGDI,BIRC6,KDM4B,MAPKAPK2,UBE2L6,PIK3R5,PIM3,DUSP16,RASA3,CHI3L1,PRKCD,ZSWIM7,FOXN3,DSTYK,POU2F3,ABCD4,CECR2,SBNO2,ZBTB47,RNF40,RNASE11,HSPA4L,NQO2,CSF3,MGLL,GLIS1,NANOG,AK5,PDE4B,MYO1F,AATK,CMTM2,VPS53,INPP4A,NFAM1,USP36,FA2H,PEX5,ANG,MED26,GSN,NOS1AP,GDPD5,LGR4,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,FCHO1,ARID3B,TOM1L2,CCDC69,DRGX,XRCC5,ABCA3,DOCK10,DPYSL3,RFX1,CPEB4,RASAL2,BLCAP,LMO7,CHI3L2,JDP2,CERS6,ACTN1,BACE1,MAP2K6,CPAMD8,PAG1,GAS8,FEZ2,SH2B2,WDFY3,ENO1,SPRED2,FAM174A,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,RNASE9,ZNF319,CYB561,SENP5,NOD2,STX1B,GRAP2,KDM7A,GJB6,MICALCL,KCNMB1,TMEM2,AJUBA,EIF4G1,SORL1,IL18BP,TJAP1,VAC14,SULF2,MYO5A,ZMYND11,C16orf70,TEX12,FAM126A,ADRA1A,FNDC3B,CALML4,DLC1,GJA8,SORCS3,CCDC92,DENND1A,TCEA1,FCHSD2,HEYL,ST6GAL1,BTBD19,SFT2D1,CATIP,MAST3,CDC42BPB,DNMT3A,CTSH,PPM1M,ZNF385C,PRPSAP1,HAVCR2,IQCG,CTNNBIP1,ANKRD33B,PDGFD,ARMC9,STXBP2,ATP11B,ZBTB17,BCAS4,CYSTM1,CCDC88C,KAT6B,ELANE,DCUN1D2,NEK6,NYNRIN,MARK3,FGD4,BCL2L15,PLXNC1,FLYWCH1,MACF1,SF3B3,FHAD1,DOT1L,IL22RA2,KCNJ15,GPATCH2,RGS3,AVPI1,TM9SF4,HLA-DMB,RBM33,SLCO2A1,RAB31,ADK,SETD1A,CPNE6,CPN1,MPRIP,WDHD1,CLCN1,CCDC34,ADPGK,TNIP3,SMAD1,GPR161,TVP23A,RGS12,MFGE8,TBC1D22A,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,TBC1D1,RNF144A,DGKI,WDR49,SERPINB13,ZNF398,SIK3,EPHA4,SLIT1,CACNA1C,HRC,SLC22A11,POLA2,SV2C,PHACTR1,EPB41,IFT140,PRRG4,WIPF3,MRPL1,LRP4,ABCC2,MBP,ELOVL3,RNF216,USP47,PPP1R13B,SCYL2,AP3M2,ERI3,ICA1,GABBR1,PPP1R1B,APBB1,CDH26,USP25,FAM83D,SMARCA2,SLC22A4,KCNN3,PPCDC,ERC2,FSTL4,ZDHHC24,NCLN,LRIG1,BPIFB1,ZNF695,ANKS6,CXADR,TMEM30A,PPM1E,IFFO1,ROBO4,VAMP1,STARD9
## 586 TFR2,ZMIZ1,TGFBR2,GSG1,RBKS,KIF5C,XYLT1,ABL1,RUFY4,CARS,ATN1,GALNT6,CELF2,COL23A1,UCK2,AZU1,VAV2,DAAM1,KIF13B,MPO,TARM1,ASB1,LPP,MGAT5,CAMKK2,POC1B,DTNB,TPP1,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,CAMK2G,PSMF1,NLRC4,CHST11,TERF2,PREX1,PRKAG2,NDUFS2,SORCS2,WDFY4,DENND2D,VDR,FIG4,TOR3A,TRIM67,LIPC,SSH1,FOXK1,ITPKC,WDFY1,IRF5,SVIL,PRKCH,PSMB7,GM2A,SSH2,MOK,FAM193B,ZDHHC14,SH3PXD2B,PPM1H,LRRK1,SLC36A1,CTSG,TTC7A,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,LPO,TNS1,TTC7B,KLHL25,GAS7,GALNT14,ACOXL,CLEC5A,GLIPR2,OPRM1,NEDD9,ZFR,MKNK1,NISCH,SFMBT2,CAMK1D,NGF,RBSN,EPB41L3,ARG1,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,PCYOX1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,SYNPO2,HSD17B12,ADAM19,KIDINS220,PPM1F,RHBDF2,CUX1,ARSG,SPARC,KIAA0586,DYM,TNF,RPTOR,PECR,FKBP5,MTAP,MEFV,LARP1,LIPA,PML,PXYLP1,ASAP2,B4GALNT3,SMG6,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,OSBPL5,HOGA1,DEFA4,MVP,PPP2R5C,EFR3B,DAGLB,TNS3,GDI2,COX10,AUH,MAST4,FTO,SCRIB,MTMR7,ARRDC5,MARCO,SFXN5,FCN1,ARL5C,AFAP1,SLC25A37,KCTD10,RGL4,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,TRPM2,PCK2,ACSL6,SIRPA,FKBP15,SYNJ2,STX8,ABCA13,ALDH2,CCRL2,NAE1,ITPR1,UBASH3B,TMEM150B,CRYL1,MIF4GD,LYN,TGOLN2,RETN,PIK3C2B,EPHB3,VTI1A,CREB3L4,LCN2,UBXN2A,LASP1,ITPR2,HIPK3,KIF21B,PCSK6,HRH1,KIAA0513,ETV6,SEPT9,MYCBPAP,FRMD4A,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,LITAF,RHOBTB2,SAG,TNFRSF1B,KCNAB2,UPB1,TFDP1,NCKAP5L,NR3C1,MCCC1,PXN,SDCCAG8,AP1G1,MYOF,POR,SULT1B1,CCDC63,RAB11FIP1,FNDC3A,CISD3,INVS,OLA1,FHIT,DISC1,GAPVD1,MYL3,TSKS,PEMT,LAPTM4A,TAOK3,RIN2,SYNPO,SLC25A35,GALNT2,MYH9,RGL1,PRTN3,PLEKHM3,KDM5B,DYSF,AKAP13,LMTK2,OXR1,CD300LG,BCL11A,XXYLT1,SLC24A4,LARS2,RAPGEF2,LAMA3,TBC1D2B,AP1G2,LIMK2,TACC3,PDE1C,RGCC,USP10,PRKCE,ZBTB20,CHST15,SLC25A18,SEMA4C,ASPH,HCN4,MERTK,SERPINA1,PSAP,SBF2,TMC8,ANTXR1,KRT17,B4GALT5,TNFRSF11A,STK39,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,ATP2B4,UST,IGFBP6,S100A12,PSEN2,BLM,IL16,HIVEP1,HEBP2,DENND3,MYADM,FGD5,AGRP,SRGAP3,RAB40C,ECE1,SLAIN1,LHFPL2,TBC1D14,PIGR,INPP5D,DOCK2,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,ERAP1,CHIT1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,TK2,CHCHD5,SLC11A1,SERTAD2,TRIO,TMC6,FAP,SAMD4A,S100A9,FAM13A,AP1B1,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,RGS14,CYTH3,RAB5C,NOL4L,TCF3,ITPKB,SNX10,UBAC2,HS3ST3B1,DNAL4,HMGCL,CTSD,TESC,PRMT5,TMEM63A,SP140,IL27,TBXAS1,ADARB1,GIMAP1-GIMAP5,GPLD1,ERGIC1,UXS1,SDC2,STK24,SYN3,CSF1,TRAF1,PLCB1,SEC22B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,TRAK1,OTUB1,PASK,IDO2,S100A8,CFAP61,FERMT3,PRDM2,DPYS,RAB11FIP3,ABCB11,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,BDH1,PI4K2A,LPIN2,HSPG2,AP3S2,HIVEP3,SLC39A11,HTR3A,ARFIP1,CRAT,PREP,RPS6KA2,ARAP2,ANXA6,OGG1,MTF1,BECN1,IL18,UGCG,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,PGS1,SCARF1,MIER2,GOLIM4,NLN,RAPSN,RAP1GAP2,MBOAT2,SWAP70,TIAM1,PANX1,LDLRAD4,RAPGEF1,ROGDI,BIRC6,KDM4B,MAPKAPK2,UBE2L6,PIK3R5,PIM3,DUSP16,RASA3,CHI3L1,PRKCD,DSTYK,POU2F3,ABCD4,RNF40,HSPA4L,NQO2,MGLL,AK5,PDE4B,MYO1F,AATK,VPS53,INPP4A,NFAM1,USP36,FA2H,PEX5,ANG,GSN,NOS1AP,GDPD5,BTD,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,FCHO1,TOM1L2,CCDC69,XRCC5,ABCA3,DOCK10,DPYSL3,CPEB4,RASAL2,LMO7,CERS6,ACTN1,BACE1,MAP2K6,GARNL3,GAS8,FEZ2,SH2B2,WDFY3,ENO1,SPRED2,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,SDHAF3,CYB561,SENP5,NNMT,NOD2,STX1B,GRAP2,GJB6,AJUBA,EIF4G1,SORL1,TJAP1,VAC14,SULF2,MYO5A,C16orf70,FAM126A,ADRA1A,DLC1,CCDC92,DENND1A,FCHSD2,HEYL,ST6GAL1,CATIP,CDC42BPB,DNMT3A,CTSH,PRPSAP1,OTUD6B,HAVCR2,IQCG,CTNNBIP1,PDGFD,SLC37A2,ARMC9,NDUFA10,STXBP2,ATP11B,BCAS4,CYSTM1,CCDC88C,ELANE,DCUN1D2,NEK6,NYNRIN,MARK3,FGD4,BCL2L15,FLYWCH1,MACF1,IL22RA2,RGS3,GLT1D1,LMF1,TM9SF4,HLA-DMB,RAB31,ADK,CPNE6,MPRIP,WDHD1,ADPGK,TNIP3,SMAD1,GPR161,TVP23A,RGS12,MFGE8,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,RNF144A,DGKI,SERPINB13,SIK3,EPHA4,CACNA1C,HRC,POLA2,SV2C,PHACTR1,EPB41,IFT140,PRRG4,WIPF3,MRPL1,MBP,ELOVL3,RNF216,USP47,PPP1R13B,SCYL2,AP3M2,ICA1,GABBR1,PPP1R1B,APBB1,USP25,FAM83D,SLC22A4,KCNN3,PPCDC,ERC2,FSTL4,ZDHHC24,NCLN,ANKS6,CXADR,TMEM30A,PPM1E,VAMP1,STARD9
## 587 TFR2,ZMIZ1,TGFBR2,C20orf27,GSG1,RBKS,KIF5C,TREM2,XYLT1,ABL1,RUFY4,SLC7A7,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,FCER2,UCK2,AZU1,VAV2,DAAM1,KIF13B,MPO,TARM1,ASB1,PCGF3,LPP,MGAT5,CAMKK2,KIAA1549L,CDCP2,POC1B,DTNB,FAM180B,TPP1,SERGEF,KIAA0319L,APP,GNG7,B4GALT1,FBN2,CAMK2G,PSMF1,NLRC4,LYPD4,CHST11,TERF2,PREX1,SLC36A3,PRKAG2,MDC1,ABCA9,NDUFS2,POLE,SORCS2,WDFY4,DENND2D,VDR,FIG4,ASGR1,TOR3A,TRIM67,LIPC,SSH1,IL19,FOXK1,ITPKC,MACROD1,WDFY1,IRF5,SVIL,TNN,PRKCH,PSMB7,GM2A,INTS6,SSH2,MOK,FAM193B,ZDHHC14,CD244,SH3PXD2B,PPM1H,LRRK1,SLC36A1,CTSG,TTC7A,SLPI,ZNF148,TGFBI,LTF,ATPAF2,CDH1,LPO,TNS1,TTC7B,IFFO2,KLHL25,GAS7,GALNT14,CDCP1,ACOXL,CLEC5A,GLIPR2,DLEU7,OPRM1,SLC10A1,NEDD9,ZFR,MKNK1,CACNA2D2,NISCH,SFMBT2,PTX4,CAMK1D,NGF,RBSN,CD82,SSBP3,EPB41L3,ARG1,CPM,NKG7,LYST,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,PCYOX1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,SYNPO2,HSD17B12,ADAM19,KIDINS220,CYB561D1,PPM1F,RHBDF2,CUX1,ARSG,SPARC,KIAA0586,DYM,TNF,RPTOR,PECR,FKBP5,MTAP,AFF4,MEFV,LARP1,BAZ1B,LIPA,UBN1,PML,NSMCE2,PXYLP1,ASAP2,B4GALNT3,SMG6,OTUB2,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,TMC7,IRAK2,FKBP9,OSBPL5,HOGA1,DEFA4,GPX3,HLX,MVP,PPP2R5C,EFR3B,DAGLB,MIR145,TNS3,GDI2,COX10,AUH,MAST4,FTO,SCRIB,RBM20,MTMR7,ARRDC5,MARCO,SFXN5,FCN1,ARL5C,AFAP1,SLC25A37,KCTD10,LRP3,RGL4,TRIM27,NDRG1,JARID2,DYNC1H1,ENC1,RPN1,MYO18A,ANKFY1,TRPM2,PCK2,ACSL6,SIRPA,PCOLCE2,FKBP15,SYNJ2,MEGF6,STX8,GATAD2A,ABCA13,ALDH2,ZNF791,CCRL2,NAE1,ITPR1,UBASH3B,BTN2A2,TMEM150B,IL18RAP,MED29,CRYL1,RCVRN,MIF4GD,LYN,SIRPG,TGOLN2,RETN,PIK3C2B,EPHB3,VTI1A,CREB3L4,LCN2,UBXN2A,LASP1,ITPR2,RADIL,HIPK3,KIF21B,PCSK6,HRH1,KIAA0513,ETV6,SEPT9,MYCBPAP,PRPF6,GGT1,FRMD4A,SH3BP5,AIF1L,HDAC4,BEND5,MGRN1,LRRFIP1,ADCY9,LITAF,RHOBTB2,SAG,TNFRSF1B,KCNAB2,NAV3,UPB1,TFDP1,NCKAP5L,NR3C1,VIT,MCCC1,PXN,SDCCAG8,AP1G1,MYOF,GPR68,NID1,POR,SESTD1,SULT1B1,CCDC63,MAML2,WDR20,RAB11FIP1,FNDC3A,CISD3,INVS,OLA1,FHIT,DISC1,GAPVD1,MYL3,MORC3,TSKS,PEMT,CCDC102A,LAPTM4A,TAOK3,RIN2,SYNPO,SLC25A35,GALNT2,MYH9,RGL1,PRTN3,PLEKHM3,KDM5B,DYSF,AKAP13,LMTK2,SLAMF8,OXR1,RFX3,LINGO1,CD300LG,BCL11A,GPR55,XXYLT1,SLC24A4,EPHA2,LARS2,CUL4A,RAPGEF2,LAMA3,TBC1D2B,AP1G2,LIMK2,TACC3,PDE1C,ITGAE,RGCC,USP10,SNAPC5,PRKCE,ZBTB20,CDHR2,CHST15,PDZK1IP1,SLC25A18,ART5,TM4SF4,SEMA4C,GSG1L,ASPH,HCN4,NXPE3,MERTK,TSHZ3,SERPINA1,PSAP,SBF2,TMC8,ADAMTS8,ANTXR1,GGT6,KRT17,ITGA5,AKAP2,B4GALT5,STOX2,TNFRSF11A,STK39,ATF7,SIPA1,HMBOX1,SCN8A,DUSP3,SORT1,SLC43A2,ATP2B4,SLC38A1,UST,CYP3A7-CYP3A51P,NFYC,IGFBP6,S100A12,PSEN2,BLM,IL16,RBM47,RFTN2,HIVEP1,HEBP2,DENND3,SLC16A10,MYADM,FGD5,AGRP,FAM53B,ZNF827,SRGAP3,RAB40C,ECE1,KCNC4,INHBE,SLAIN1,LHFPL2,SAP30BP,TBC1D14,PIGR,INPP5D,IL6R,DOCK2,MECOM,OLFM4,CBFA2T3,DOCK4,TRAPPC9,ARHGAP26,PKD1L1,SPRYD4,CLDN15,SURF6,RERE,VNN2,ERAP1,CHIT1,BCR,CREB3L1,FMNL3,ABR,MAD1L1,TK2,CHCHD5,SLC11A1,UNC5B,SERTAD2,TRIO,TMC6,FAP,TNFRSF9,SAMD4A,S100A9,FAM13A,AP1B1,PHF11,GFI1,CEP164,PHACTR2,LTA4H,PPIL2,ADAP1,SLC2A9,RGS14,CYTH3,BTBD11,RAB5C,PLXND1,ITGA9,NOL4L,TCF3,ITPKB,SNX10,UBAC2,SLC39A10,HS3ST3B1,DNAL4,HMGCL,CTSD,TREM1,TESC,PRMT5,TMEM63A,SP140,IL27,TBXAS1,IL1R1,ADARB1,GIMAP1-GIMAP5,HHIPL2,NAV2,GPLD1,ERGIC1,UXS1,LY6H,SDC2,SLC45A4,PRR5L,STK24,TMEM182,SEMA4A,SYN3,SUSD6,CSF1,TRAF1,RAD54L2,PLCB1,RAD9B,SEC22B,CDK6,RMI2,ALS2CL,LOXL2,ERN1,DEDD2,TRAK1,OTUB1,SETD2,PASK,IDO2,S100A8,CFAP61,FERMT3,PRDM2,DPYS,RAB11FIP3,ABCB11,ELL2,FPR2,ZNF385A,HDLBP,NOTCH1,PARP15,BDH1,ZNF516,ECM2,PI4K2A,LPIN2,KIAA0195,HSPG2,AP3S2,HIVEP3,SLC39A11,HTR3A,ARFIP1,CRAT,PREP,RPS6KA2,PLXNB2,ARAP2,EP400,ANXA6,OGG1,MTF1,SLC26A9,BECN1,SLC19A1,IL18,UGCG,SPIDR,BAIAP2,PIK3AP1,PITPNM2,PPIL6,LRRC1,PPFIA1,ATP8B1,PGS1,SCARF1,MIER2,GOLIM4,NLN,TMCO3,RAPSN,RAP1GAP2,MBOAT2,TMEM72,SWAP70,TIAM1,PANX1,C11orf45,LDLRAD4,RAPGEF1,ROGDI,BIRC6,KDM4B,MAPKAPK2,UBE2L6,PIK3R5,PIM3,DUSP16,RASA3,CHI3L1,PRKCD,ZSWIM7,FOXN3,DSTYK,OCSTAMP,POU2F3,ABCD4,CECR2,AADACL3,SBNO2,ZBTB47,RNF40,RNASE11,HSPA4L,NQO2,CSF3,MGLL,GLIS1,NANOG,AK5,PDE4B,MYO1F,AATK,CMTM2,VPS53,INPP4A,NFAM1,USP36,FA2H,PEX5,ANG,MED26,GSN,NOS1AP,GDPD5,LGR4,BTD,ADA,SLC29A3,ASGR2,KLHL3,DHODH,ATP8B2,AAK1,FCHO1,ARID3B,TOM1L2,CCDC69,DRGX,XRCC5,ABCA3,DOCK10,DPYSL3,RFX1,CPEB4,RASAL2,BLCAP,LMO7,CHI3L2,JDP2,CERS6,ACTN1,BACE1,MAP2K6,GARNL3,CPAMD8,PAG1,GAS8,FEZ2,SH2B2,WDFY3,ENO1,SPRED2,FAM174A,LRRC8D,PLCD1,RAPGEF4,HIP1,SRGAP1,WT1,MAN1C1,ARRB1,SDHAF3,RNASE9,ZNF319,CYB561,SENP5,NNMT,NOD2,STX1B,GRAP2,KDM7A,GJB6,MICALCL,KCNMB1,TMEM2,AJUBA,EIF4G1,SORL1,IL18BP,TJAP1,VAC14,GXYLT2,SULF2,MYO5A,ZMYND11,C16orf70,TEX12,FAM126A,ADRA1A,TSPAN18,FNDC3B,DLC1,GJA8,SORCS3,CCDC92,DENND1A,TCEA1,FCHSD2,HEYL,ST6GAL1,SFT2D1,CATIP,CDC42BPB,DNMT3A,CTSH,TSPAN3,PPM1M,ZNF385C,PRPSAP1,OTUD6B,HAVCR2,IQCG,CTNNBIP1,PDGFD,SLC37A2,ARMC9,NDUFA10,STXBP2,ATP11B,ZBTB17,BCAS4,CYSTM1,CCDC88C,KAT6B,ELANE,DCUN1D2,NEK6,NYNRIN,MARK3,FGD4,BCL2L15,PLXNC1,FLYWCH1,MACF1,SF3B3,DOT1L,IL22RA2,KCNJ15,GPATCH2,RGS3,GLT1D1,LMF1,TM9SF4,HLA-DMB,SLCO2A1,KIAA1549,RAB31,ADK,SETD1A,RGSL1,CPNE6,CPN1,MPRIP,WDHD1,CLCN1,ADPGK,TNIP3,SMAD1,GPRIN3,GPR161,TVP23A,RGS12,MFGE8,ANKS3,CD209,RAP2A,IP6K3,DOCK1,SPTB,TBC1D1,RNF144A,SLC6A6,DGKI,SERPINB13,ZNF398,SIK3,EPHA4,SLIT1,CACNA1C,HRC,SLC22A11,POLA2,SV2C,PHACTR1,EPB41,IFT140,PRRG4,WIPF3,MRPL1,LRP4,DIP2C,ABCC2,MBP,ELOVL3,CACHD1,RNF216,USP47,PPP1R13B,ANO10,SCYL2,AP3M2,ICA1,GABBR1,PPP1R1B,APBB1,CDH26,USP25,FAM83D,SMARCA2,SLC22A4,LYPD8,KCNN3,PPCDC,ERC2,FSTL4,ZDHHC24,NCLN,LRIG1,BPIFB1,ZNF695,ANKS6,CXADR,TMEM30A,PPM1E,IFFO1,ROBO4,VAMP1,STARD9## [1] 1563 8write.table(gem, file=file.path(res.dir,
paste0("gProfiler2_cra_camp_logIgE_DMPs_enrich_hyper_", timeStamp, ".txt")),
sep="\t", quote=F, row.names=F)
table(gem$Domain)##
## CORUM GO:BP GO:CC GO:MF HP HPA KEGG MIRNA REAC WP
## 1 584 161 93 296 351 10 42 20 5path.hyper <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hyper)## [1] 35 8#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hyper, filter = 'top')enrich.hypo <- gprofiler2::gost(query=uniq.hypo, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))## Detected custom background input, domain scope is set to 'custom'# for results containing all annotated terms
gem <- enrich.hypo$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
head(gem); dim(gem)## GO.ID Description term_size
## 3776 MIRNA:000000 MIRNA root 14165
## 1824 GO:0005515 protein binding 13924
## 1825 GO:0005488 binding 15946
## 1826 GO:0003674 molecular_function 17356
## 1561 GO:0005622 intracellular anatomical structure 13844
## 1562 GO:0005737 cytoplasm 11268
## intersection_size Domain FDR Phenotype
## 3776 2667 MIRNA 1.480722e-154 +1
## 1824 2578 GO:MF 1.904534e-125 +1
## 1825 2813 GO:MF 1.904534e-125 +1
## 1826 2959 GO:MF 2.615815e-125 +1
## 1561 2545 GO:CC 3.977935e-115 +1
## 1562 2203 GO:CC 5.258750e-113 +1
## Genes
## 3776 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,TTC7A,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,NHLRC4,KIAA1522,GNB5,TMED3,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,SLC29A1,EHD1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,ELMO1,GPR176,FBXW8,MITF,SLC25A33,ABCC1,SLC7A1,TNIK,TRIM9,DAPK2,TFF2,GFOD1,IL5RA,OSBPL5,TRIO,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,IL4,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,NKIRAS2,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,SLC2A8,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,PNN,SLC24A3,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CBFB,EPHB2,TTYH3,CHP1,VPS53,ZNF48,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,C6orf132,ERMAP,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,ITGAL,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,SLC45A4,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,TRIM33,UBE3B,HEXA,MTMR3,SH3GL1,NCOR2,ENTPD1,SLCO3A1,SSBP3,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,GALNT10,NVL,TPST1,POR,AXIN1,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,INPP5A,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,ADORA3,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,NSMCE1,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,CCDC127,HK2,DYRK1A,MLX,BATF2,DAG1,KRT8,LGALS8,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,PLXNA2,ANKRD52,SERINC5,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,WWP2,P2RY2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,BACH1,MAP6D1,C11orf24,DPH7,ACSL1,ABR,DOCK1,BCAS1,NEMF,RAB11FIP1,SPNS3,MAP1LC3B2,BDH1,FHL2,CMBL,RALGDS,NUTF2,TANGO2,ELMO2,COL15A1,SLC2A9,GJB3,SGMS1,SPATS2L,POLR2F,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,SLC41A1,FOXJ3,HMGCL,KLF16,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,AQP1,GPR156,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,FBXO7,ABCB9,CCDC85C,GRAMD1B,CALML4,PELI2,PHLDB3,SIAH2,MICAL2,MYLK,TMOD3,SAP30L,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,AMZ2,ZNF70,IL13,CCNY,DMAP1,SLC23A2,PRX,RREB1,ERGIC1,TMEM154,ABCC4,ADAMTS14,PDE4B,GNG12,PI4KA,NADK,ZC3H11A,SLC12A4,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,CATSPER4,RNF40,ZKSCAN5,RBL2,GSN,TRAF3,LTBP4,SEMA3B,MFAP4,TPCN1,MCM2,CAB39,GALM,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,THYN1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,PPP1R16B,NCK2,RNF157,IKZF1,HECW1,MAML1,SLC29A3,SULF2,GSTM3,TGFA,GALNT12,CEBPB,STK3,ARID1B,PTGDR2,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HTT,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,FAM53B,BAIAP2L1,SPTBN1,MYL9,GLB1,TNXB,DENND5A,ST3GAL1,XYLT1,CD86,SOAT2,FMO1,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,UNC5B,NEDD4L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,SOGA1,ZNF532,SIK3,EML3,VSIG10,ZSWIM3,SNX9,LRRN2,BCL7A,SLC43A3,MCMBP,DNAJC3,WNT3,GALNT7,UXS1,MTUS2,DHCR24,PHF13,C19orf54,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,TMEM116,NFATC2,ZHX2,TMEM104,NXF1,SLC2A6,CACNA2D1,NELFCD,ABHD2,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,PIGN,CDKN2AIPNL,WDFY2,RNF216,AGAP3,BACH2,CORO2A,EFNB2,ATG13,NEK8,PHTF2,LARP1,TBC1D9B,CACNA1D,KBTBD4,CHRNE,LRRC8C,P2RX7,SLC11A1,PIK3AP1,LINC00548,P3H2,C1QTNF1,VPS13D,OSBPL3,ASNSD1,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,AJAP1,TPM3,CCDC57,NBPF8,STON1-GTF2A1L,PLLP,UBE2G1,PRKDC,DESI1,RFT1,GAS7,MBTPS1,HK1,RIN3,SLC7A11,MLST8,JAG1,XAF1,DNHD1,ERG,IMPA2,VAMP1,AGXT,NAP1L4,GTPBP1,CLDN10,VGLL4,GTSF1L,GON4L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,NAV2,MAPRE3,LRRC8D,PSD3,ASB8,ZDHHC18,SMYD3,IL34,RPH3AL,NUDT1,FOCAD,DSC1,LBR,NDRG1,ADAR,ACAD10,SMG6,RHOBTB2,SECISBP2L,SND1,MBD6,RCC2,PAFAH2,SLC45A3,SLIT3,USP19,FAM135B,ITPRIP,DCAKD,IL18BP,SREBF2,ASIC1,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,THRB,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,COL4A1,ARL15,SELPLG,LEF1,OSBP2,LRRC20,FAM104A,RIBC2,PRNP,RHBDD2,C16orf70,SPATA21,IQCD,DHX30,PRDM10,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,MIDN,VEGFB,B3GALNT2,THADA,NRG2,SDK1,MDM4,ELL2,ZDHHC7,RAPGEF1,CTSK,PDZD8,HDAC4,EXT1,ACTN4,EPN2,ARPP19,GPD2,C16orf45,FCGR2A,SUSD6,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,ITGA2,OPA3,HNRNPM,SIPA1L3,RMND1,PPP1R2,ARL6IP4,CTSZ,PTPN18,LGR5,INPP5F,IL1B,AFF1,WDR73,ADCY9,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,PTPN1,B4GALT7,AAK1,LIMK1,CDK5RAP3,FBXL2,RAB3B,EHMT1,ZXDC,ABAT,ANO6,IKZF2,STOML1,POMGNT1,TSPAN2,CD81,KIAA0232,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,TOP1MT,RALY,DIDO1,ZNF175,LCP1,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,SLC7A7,ATP2C1,RNF43,EHBP1,HPS4,CHCHD3,ZNFX1,ARSB,FBXL13,IP6K2,GRB2,EMC1,FOXN3,TAOK2,MCPH1,POC1A,LAX1,GPR35,KLF13,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ZSWIM4,ERP29,ADAM19,PCCA,TBL2,STT3A,KIAA0040,TMEM156,CDX1,DHX37,MVB12A,CLK3,TBC1D2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,NINJ1,CHST11,DGKG,MBOAT1,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,MTA2,PLD5,PADI2,KCNIP2,SIL1,LSM14A,INSC,LFNG,GDPD5,MYO9B,MYLK4,DNAJC18,SUPT3H,PPP2R5C,OPALIN,ERI3,SLC35D1,RNF24,CD4,TLE4,TTC17,USPL1,DNMT3A,RBM33,MACF1,SRF,ZBTB34,TMED10,LGR6,AACS,P4HB,MICAL1,ACAD8,MRPS27,TUBGCP2,TRPV6,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,FNDC3B,GUCD1,MTFR1,ERAP2,ODC1,FBXO34,YWHAQ,CSDE1,COLQ,IQCE,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,IL1RN,PLEKHA7,SLC39A2,OAF,ZBTB42,DNAJC6,ACO1,WDR46,GABARAPL1,SHBG,MAPKAPK3,CHD9,SLC7A14,NHSL1,HECW2,SERF2,UGGT1,EXD2,SMG5,EARS2,SF3A1,TESK2,ATG7,ACSF2,SCAF11,RHOH,SRC,PCBP2,SLC13A2,SACS,MTHFD2,PAG1,TBXAS1,CRTC3,TAS2R5,PDE4D,SPI1,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,DDX56,DHX15,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,EPC1,PPP2R5E,RFC3,TRIM16,MARK3,NACC2,CAMP,BBS1,RASSF5,ATXN1,TMEM41A,ARID5B,HDAC9,SLC44A4,TMCC2,ARFGAP2,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,SLC25A45,MBNL2,ADORA2A-AS1,MCCC2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,SIN3A,STIM2,KIF26A,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,BCL9,FAIM2,VDR,SLX4IP,RAD21,CEBPE,CFAP45,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,DEPDC1B,SKI,KCNE1,PPM1A,NMUR1,HIF1A,SAG,ILKAP,TNRC18,HIVEP2,EIF4EBP1,FAM107B,EEF2K,TRPM4,TMEM131,NCOA7,ASH2L,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,ART3,PDE4DIP,CPD,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,HMGXB4,SLMAP,PTP4A2,CCDC136,AGPS,KIAA0100,LDLRAD3,PQLC2,ST3GAL2,BICD1,LSM3,TCF7L2,CDC42BPB,ORAI2,AHCYL2,CUX1,LHPP,TXNRD2,RNF149,MUC20,TMEM220,AKR1E2,PSMC1,MCC,MTURN,LSM2,ZBTB12,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,RPRD1A,CFAP43,EFHD2,RFX2,PSMD6,SPIDR,MAP3K14,BANK1,SART1,WDR70,ZC3H7B,SLC25A3,PLAGL1,ICAM3,AP1M1,SLC2A5,ITGB3,TMEM51,TRAPPC10,TOP1,AGO2,CNOT10,LONRF2,MAML3,NR1H3,GZF1,MTA3,NIN,GOLGA3,HNRNPLL,ARRDC2,WDR8,TMEM241,MED15,PRG3,CARD11,HECTD4,RASSF4,MAK16,GAPVD1,EPB41L2,POLR1C,GSE1,GNAI1,NR3C1,NAA25,HAVCR1,SCOC,ZNF563,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,CRISPLD2,CCDC50,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,GALNS,SLC39A7,TOR2A,EPHX4,NT5E,UST,ZRANB1,OSBPL6,TRIM71,EFR3A,SLC39A3,SRPK1,BEND6,RBM14,AGER,NANS,ETV6,YEATS2,VPS52,E2F7,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,PTDSS1,FBXW11,OLFML2A,MIEF2,LOXL1,OGDH,ZZEF1,CTDSPL,PAM16,MAN1A1,RAB40C,NUP93,ADGRV1,TRIM26,SLC22A23,SPPL3,EYA3,PROCA1,SDCCAG8,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,REV1,PEBP4,DYRK2,RXRB,HNF1B,PLEKHA6,DDX27,LDB2,DMXL1,ATXN7L1,GALNTL6,STAT4,TRAF1,F5,MAPK1,ST6GALNAC4,KLHL29,USP39,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,SFMBT1,PIGV,BAZ1A,TMEM123,SUSD1,PHF1,HSD17B12,SIRPG,PTPRC,AP2B1,C6orf47,ZC3H14,RANBP3,SPATA5,ARAP1,POLR1A,TUBD1,N4BP2L2,RNF103-CHMP3,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,ABHD12,NOTCH2,SEPHS1,CYB5R3,SMURF2,DTD1,ADGRG6,EPHX1,SHMT2,VANGL1,ADRBK2,ARID4A,PELI1,LIMD1,CHST15,HCN3,SPIRE1,RAB7A,TCF7,SPTBN2,SCN4A,ARHGAP10,HLCS,PEX2,STX2,KLHDC7A,L3MBTL1,IDO1,NAA16,BHLHE40,GPD1,TXNDC11,PIWIL2,CELF2,FYN,UPF1,ADAP1,POLR3A,SIAE,THEMIS2,ABTB2,MED13L,ANKRD11,SPOP,LRIT3,HADH,FAM83A,PPP3R1,STK10,LSG1,KIF6,GID8,ZC3H7A,RNF13,EPAS1,CPM,PER2,ASAP2,WWC2,ERMN,ARL6IP6,TRPM3,TMEM63A,TRIM29,EIF1AD,PCGF3,PIK3CB,GNS,SPECC1,NAT9,RAB19,CLMN,STAT3,SLAMF1,SYN3,MEF2C,MAP4K5,EEFSEC,PYCR1,BUD13,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,GRK4,TMEM17,TIGD1,CXCR4,TMEM201,DAZAP1,PGM1,IMMT,SIGLEC10,CEP128,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,CACNB2,COL4A3BP,IDNK,TAF6,MAP4,DNAH3,ARHGAP12,RMDN3,EFCAB5,ARFGEF2,MAP3K8,VEGFA,EME1,LRCH1,UQCRH,CPA1,ADAM12,MN1,LCLAT1,PLEKHM3,FTL,PRDM16,FAR2,CPEB3,CDK14,TMEM203,FAM102A,APP,GPSM1,SEC62,PRIM2,THAP4,YARS,SUSD4,RASSF1,SLC35C1,IGF2BP2,SENP7,CRB1,AUTS2,CHSY1,XPO6,RUNX3,PDXDC1,ZNF852,ZFYVE21,LAPTM4A,FADS1,RALGPS1,SRP68,DBNL,PLA2G4F,MAST2,PHF21A,CRTAM,GDA,ZBTB16,SYK,C1orf174,MAPKAP1,ADIPOR2,TIMP2,RFFL,H6PD,AFF3,RIOK2,OR6B1,CDK2,CYSTM1,CHPT1,RPS6KA4,ECHDC1,GPR107,ANXA2,PPARA,GTPBP2,EIF3M,GNB1,KRT71,FGF1,JMJD1C,AGL,ELOVL6,SIK2,SNX10,ANTXR2,YWHAE,PHACTR2,WDR1,AKT3,JAZF1,SDC1,DNAJB13,PTH2R,TLE1,OLA1,CACFD1,SLC12A6,GNAI2,YES1,EXOC6B,TSPAN33,EREG,GPC5,RBM19,CPPED1,SMPD3,MLLT1,PHACTR3,CPSF6,CREM,GRHL1,SIAH1,ACVR1B,SPAST,ALKBH5,CALD1,PTK2,C15orf48,MBD5,AMBRA1,SLC4A1,HDAC11,ERN1,CCDC12,BASP1,RBPJ,RHOA,ARHGEF3,C2CD3,DOCK4,TOLLIP,IKBKB,PSMD13,C12orf76,TPPP3,FER,KLF7,FANCA,PDE6B,SNUPN,SETBP1,MRPL10,ZCCHC14,STUB1,RDH5,CDK19,CES4A,CYTL1,IGSF3,CAPZA2,PHC3,ENTPD7,KAT5,CEP85,SIPA1L2,CTSA,MAML2,SETD2,PTPRN2,SDK2,TALDO1,CD160,MFSD10,DEDD,FOXO3,CAPN7,FUT4,URGCP-MRPS24,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,FBXO36,BSCL2,CDCA7,PARN,COL1A1,ATF7,SEC23B,TRAPPC3,NUP210,OTOF,FAM118A,TGFBRAP1,IRF2,TIMM22,GSK3B,YWHAZ,SSTR1,SERGEF,SLC38A6,GMEB1,DGCR2,TREM1,EMILIN2,ZC3H4,MAPKAPK2,ORC1,TM7SF3,RHOBTB3,CHD7,TJP3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,C16orf58,CBY3,RBM34,PAX8,DPP9,CPNE2,SUCNR1,MPV17,PALD1,ASAH2B,ZCCHC24,CLCN6,NME2,CD300LB,VTI1B,NPM3,SMCO4,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SLC7A6OS,SARM1,CSRNP2,SHE,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,ATP1A1,CTLA4,FAH,TAGAP,PGD,UBXN7,MYB,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,FAM89A,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,ECHDC3,KLHL3,ADK,TMEM99,IGF2R,CRTC1,MYT1,UBR1,PHC1,GCNT2,LRCH4,NET1,MAPRE2,NEK7,C10orf88,FARP1,PBRM1,STAMBPL1,AMFR,ACSF3,RAB25,CNNM3,RCOR1,RAD51B,CCL26,UBA7,MYO10,LPCAT1,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,HOXA3,RXRA,NOD1,TAOK3,ACADL,PARD3B,MYO1H,EPSTI1,PNRC1,PRKG2,CSNK1G3,FAM110B,TMEM117,KHDRBS3,EDEM2,SCARF2,XPC,GNA13,ABCG8,ALDH1A2,MYOM1,HNF4A,ISM2,KANK1,PLCXD2,WNT3A,TTC28,UBAP1,KRT6B,NR6A1,CXXC5,RNF121,FNBP1,RBMS1,TAF15,CERK,STX16,DNMT1,TYSND1,MAFF,WEE1,NUGGC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ARHGAP11A,ZFHX3,REPS1,ALDH3B1,PBX1,ATP8B1,SHROOM3,UNC79,KIF21B,VEZF1,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CNGA4,CCDC86,ADCK1,RPL36AL,TTL,CAMTA1,PIGS,NOL10,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,SP110,TP53BP1,ASPSCR1,C14orf43,PRKCA,RCC1,GLRX5,MDFIC,CCND3,FTO,MARK2,ATP10B,GPR183,CLPB,LCORL,FAM168B,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,BTBD9,UPF3A,FXYD1,GET4,SETD5,NFASC,GRK5,TBC1D14,CUX2,RASAL2,COG7,TEX2,EFNA5,ZNF865,AGPAT3,SHB,HPS1,ATP8B2,STX17,SPRED3,CNPY3,XPNPEP3,SORBS2,PDZRN3,ANKRD10,DCTN2,CXCR6,TPST2,SHPRH,BATF,GEMIN5,RDM1,MYO1A,SLC39A1,RHBDD1,FAM207A,FCRLB,ADAM9,FDFT1,PARP4,GLE1,METTL9,GSTM4,NSMCE2,KDM4C,NEK6,CREB5,UBE2QL1,BRCA1,TMEM245,ITGB5,MNDA,ZNF507,SERPINB6,TTLL4,HPCAL1,C4orf45,NLRX1,PSMB7,SGK1,METTL8,RAB11FIP3,PPRC1,CPSF1,STXBP2,OSBPL8,STAT5B,RRP9,PNPLA2,RNF138,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,ITGA11,SP2,RGL1,LIG3,NCAM2,SORL1,TRPM2,RSU1,MCF2L2,DCTN5,MFSD12,TAF5L,ALPL,LHFPL2,CTDSPL2,FNTB,TET2,C10orf105,ZKSCAN3,NDUFA4,ATP6V0A2,PIEZO1,ALPK3,SAMD8,MT2A,SMYD4,CLEC16A,HIBADH,MX1,TRAK2,CKS2,FURIN,UNK,YDJC,WWP1,GTF2F2,MRC2,SLC25A13,SNTB1,RAB7L1,FRYL,DRAP1,ARPC4,SLC13A4,SLC16A3,RPA1,FANCC,HCRTR1,SMAD5,ANXA4,SIRPA,TOX,KMT2D,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,KLRD1,BAHCC1,PEX11A,ECM2,ACSL6,STARD10,POPDC2,MYCT1,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,UBE2K,EVI5L,TGFBR2,TULP4,CD82,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,PPM1L,ZNF215,GNA14,NUSAP1,ZFC3H1,LYRM1,EHD4,PTPRF,LEPROTL1,ITPR2,SLC38A1,EXOC4,TG,MYEOV,FEM1C,RNF145,DCUN1D1,GREB1L,ZBTB7A,USP46,DHRS4,MYO5A,FAM174B,FBN1,RET,DUS2,TCF4,RNF11,ZNF827,CHCHD6,ZNF710,DNAJA3,ARHGEF4,MDM1,CCAR1,REXO2,FAM81B,ARHGAP35,ANP32B,LRP1B,ANKRD44,EDRF1,BCL7B,TMEM130,SHANK2,NFIL3,EEPD1,DLK1,ZBTB20,ATAD5,MKNK1,IRF7,MAT2B,HSPG2,C11orf48,PRIMPOL,BNIP3L,KCNK6,ATP6V1H,ARID2,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,IL18R1,KIF13B,KCNK10,SLC16A10,STK24,ENPP2,BET1L,CCDC74B,ANKRD6,GPR132,FLT3,WDR37,PM20D2,LRP4,ZNF638,SLC30A1,RRBP1,GLUL,TTC22,ANKS6,FAM117A,PIGR,MATN1,AKIRIN1,HRH2,PDE7A,ETV3,TRAPPC12,DHX8,APOLD1,NRXN3,VRK1,PARP16,EDARADD,RSPRY1,ART4,NLK,FSTL4,SLC38A10,C11orf68,TGM7,KDM6B,TNFAIP1,RCSD1,CERKL,PPIC,TLL2,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,PLD4,LUZP6,HIF1AN,BAG2,KIF5B,LMO2,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,ITGB6,LGR4,CABLES1,SCAF8,DCLK3,PRPF38B,IL18RAP,BUD31,UTRN,CSRP2BP,RFC4,ATP2A2,STK11IP,FRY,MDN1,AKT2,PRDX3,KLRK1,ANKH,MPL,DCP2,SIN3B,HRK,C6orf89,TBL1XR1,PARP10,ZNF131,MCFD2,URGCP,CCDC141,NEIL2,CRIM1,SNRNP70,TRIM2,ZNF552,TRAM2,DCBLD1,FNIP1,TP53BP2,LAPTM4B,FAM91A1,MOB1A,PIAS1,CLYBL,IVNS1ABP,KNDC1,JDP2,RALGPS2,ARSK,ZSCAN12,SRSF7,RAB3IL1,ZBTB17,SGPP1,PARP1,NCAPD2,ZBTB38,SLC4A8,ACTRT2,CYBRD1,NTAN1,MEGF11,MFF,LRRC42,ITGB4,TRPM7,FRMD4B,CDH18,TMEM79,SLC37A1,PRDM2,CAT,OSBPL10,FBXW7,MERTK,LILRA1,HNF1A,PSMD1,SCG3,CDC25C,RAD52,MTSS1,PLXNC1,NR1I2,LRFN1,RUNX1,SNX4,TACR2,ZSCAN25,CRLF3,ZC3H12C,SGIP1,STAT6,SNX30,FNBP4,CTDSP2,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SEL1L3,HS6ST1,NECAB1,EZR,AHI1,TMEM64,CTSS,GABRR2,STARD3,DUT,GNPNAT1,CCDC96,RNF130,ARHGEF10L,LRRFIP2,ZNF333,AAR2,PLA2G4A,CA12,ATG16L1,CMTM7,MTA1,CLTC,IFFO1,CKLF,KIF13A,BBX,TNIP2,RFTN2,MYLIP,SPEF1,SLC25A38,RPGRIP1,MAMDC2,SLC11A2,DENND1B,HAL,LYN,CENPJ,AKAP2,SERBP1,GAS2L1,ACP6,AKT1,ACR,GRAMD4,UBTD2,TBC1D31,UBXN1,UNC50,KPNA4,SLC1A3,ASXL1,TSPAN31,IL1RAP,ATXN7,PEX14,PDE4C,ALPK2,RRS1,MAPK6,DOK4,MOSPD3,TFB1M,GPR39,ST3GAL6,ZADH2,HIPK3,METTL1,LTC4S,CASKIN2,GULP1,PPTC7,CARD14,ALS2,DTNA,ZNRF2,INPP5D,RAPGEF3,NR2F6,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CUEDC1,CLCC1,NCOA2,ACTB,PIGC,TOP2B,ORAI3,CLEC17A,BAIAP2,TNFRSF9,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,PDIK1L,WT1,ST3GAL5,SMPDL3A,ATG10,COPA,ARHGAP9,DNAJC5,CEP83,CSNK1G2,RPS15A,ASB2,TRABD,CLEC12A,DST,MORF4L1,CLSTN1,PSMG1,ANKRD13B,PCNA,DHRS11,LETM1,LPIN2,UBE2E2,PHB2,TLK1,PDLIM2,BUB3,C1RL,MPPED1,NACC1,LITAF,MYO1F,TMEM19,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,ETV7,SEC24A,PSPN,DIXDC1,TNFRSF10B,MDGA1,SFI1,LIPC,KDM2B,HCLS1,MAP2K6,CREB3L1,FBXO9,IL10RA,LRCH3,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,ADIPOR1,NDUFS6,RABGAP1L,PKD2,ZNF704,USP1,NARS2,MSRA,ATL1,PAX7,ZMIZ1,DRD2,CD47,EFR3B,TMEM184B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,NFIC,UHRF2,C1GALT1,PPP2CB,PEX7,ZNF652,PLAA,IL15,ARNT,NEURL1B,SERPINF1,SLC25A10,TMEM45B,TMEM168,CPA3,PGAP2,JPH2,DNAJC13,RAB27A,BRD7,ATAD3C,MIA3,GMPPB,A2ML1,ARID4B,PFKFB4,C1orf122,CEP295,ALOX5,EHMT2,ZBTB10,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,CGN,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,EIF4G3,SMCHD1,OAT,MGST2,DLGAP4,LRP12,FYCO1,C17orf63,MS4A6E,MICU1,SEMA3F,RBFOX2,DCTN4,EAF2,PEAK1,FLOT1,CAND2,YOD1,NOX3,LMNB1,CXCL3,APLF,LIMCH1,GLYCTK,THSD7A,CNKSR3,LOC81691,WIZ,ZDHHC14,ELF1,TSPAN14,STAU2,NFE2L1,DGAT2,DLC1,ATXN10,OTULIN,PRR5,YY1AP1,PPP2R1A,CCL28,TMEM50B,DYM,KPNB1,KCNN3,KRI1,CLPTM1,B3GALNT1,NUDT19,GPRC5A,CDH22,ALDH6A1,GALNT11,CDYL,ACVR2A,DBN1,HSPD1,HMOX2,COLGALT2,HIVEP3,TBC1D13,PWWP2A,OIT3,MAP3K4,NAPG,ALCAM,EDEM3,PROK2,CARS,ARMC2,RAB8B,CHST3,RAP1A,TNPO1,MTF1,RASGRP3,PSEN1,MRPL16,SGSM2,SMYD5,P2RY6,SOX6,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,PPP1CA,INTS8,SEC63,FDX1,MPRIP,REEP5,ITFG2,NGLY1,GIT2,USP47,SPIRE2,ZNF516,SPTLC2,KLHL5,KLHDC4,RASSF8,ZEB1,WDR7,SEMA6D,GMDS,PGS1,C5AR2,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,SBSN,RNF19A,CPT1A,MNT,SEMA4C,GSPT1,QKI,ARL2,DEFB125,BTN3A3,ALG14,FKBP1B,MRPS14,PWP2,BATF3,IQGAP1,CCDC112,AMPD2,AFTPH,ACIN1,TOR1B,HBS1L,ANKRD9,NCAM1,ATF6,INPP5E,PDPK1,SLC25A44,MAP2K3,PLCB1,GALNT18,ADD3,CD84,BIK,NUCKS1,ELP6,PRPF8,PACS2,MON2,ALAD,PANK1,CCDC146,RPS6KA1,NEK1,NMNAT1,GTDC1,KIF3B,SUFU,STX1B,CNST,GRK6,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ZZZ3,TGIF2,ESYT2,SLC40A1,GALK2,CACHD1,ZFAND6,RASA2,RB1CC1,DFFA,PKNOX1,RCBTB2,COG2,IL2RA,RUNX2,NCLN,ST14,PAK2,ALAS1,FLT1,CLCN7,DOCK10,FBL,EMID1,GCNT3,ZNF565,C1orf9,PRKAR2A,ZNF740,PCM1,RNASET2,MTMR7,TRPM5,TNFRSF13C,ZNF518B,ZFAT,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,C1QTNF6,MARK4,C9orf64,DHX33,PIK3R3,ASB3,JADE2,MAP3K5,ATP6V0D1,ZMYND8,BCAS4,DTHD1,KLHDC3,NPTN,SORBS1,PIKFYVE,CAMK4,KIAA1549,DDA1
## 1824 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,FBXW8,MITF,SLC7A1,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,TRIO,TRIM4,UBE2O,ARID3A,FOXJ2,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,TESC,USP32,TRPC4AP,IGF1R,TRAPPC9,UVRAG,MUC13,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GNAO1,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,SSBP3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,COTL1,CLIP1,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,TPST1,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,INPP5A,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,NSMCE1,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,MAP3K1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,WWP2,P2RY2,FADD,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ABR,DOCK1,RAB11FIP1,PRKAG2,MAP1LC3B2,FHL2,DAB1,RALGDS,NUTF2,CCL18,ELMO2,SLC2A9,GJB3,SGMS1,SPATS2L,GLYR1,SLC18A2,DPPA3,SLC41A1,FOXJ3,CLRN1,KLF16,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,FBXO7,ABCB9,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,MYLK,ADTRP,TMOD3,SAP30L,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,IL13,CCNY,DMAP1,ZNF789,PRX,ERGIC1,TMEM154,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,SLC12A4,PROZ,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,CATSPER4,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,MFAP4,TPCN1,MCM2,KEL,CAB39,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,TNN,PPP1R16B,NCK2,IKZF1,HECW1,MAML1,SLC29A3,GSTM3,TGFA,CEBPB,STK3,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HTT,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,BAIAP2L1,SPTBN1,MYL9,GLB1,TNXB,DENND5A,LGALS4,HK3,CD86,SOAT2,FMO1,MAN1C1,RAP1GAP2,MED12L,UNC5B,COL20A1,NEDD4L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,SIK3,EML3,VSIG10,ZSWIM3,SNX9,LRRN2,BCL7A,SLC43A3,MCMBP,DNAJC3,KAT8,WNT3,UXS1,MTUS2,DHCR24,CDH23,EVPL,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,TTLL6,NELFCD,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,CDKN2AIPNL,SERP2,WDFY2,RNF216,TBC1D10A,AGAP3,BACH2,CORO2A,EFNB2,ATG13,NEK8,CD7,LARP1,TBC1D9B,CACNA1D,KBTBD4,LRRC8C,P2RX7,SLC11A1,PIK3AP1,P3H2,C1QTNF1,VPS13D,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,AJAP1,TPM3,CCDC57,CALR3,PLLP,UBE2G1,PRKDC,DESI1,RFT1,GAS7,HK1,RIN3,SLC7A11,MLST8,JAG1,ST7,XAF1,DNHD1,ERG,IMPA2,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,HPX,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,NAV2,MAPRE3,LRRC8D,PSD3,ASB8,SMYD3,IL34,RPH3AL,NUDT1,FOCAD,DSC1,LBR,NDRG1,ADAR,HVCN1,SMG6,RHOBTB2,SECISBP2L,SND1,MBD6,RCC2,SLIT3,USP19,ITPRIP,IL18BP,SREBF2,ASIC1,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,DGKI,NLRC5,RBX1,THRB,SGSM3,TGFB3,EIF6,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,NAPA,LEF1,OSBP2,LRRC20,FAM104A,RIBC2,HDC,PRNP,RHBDD2,C16orf70,IQCD,DHX30,PRDM10,THG1L,KRT72,ATP2A3,AHNAK,MIDN,VEGFB,DNAH1,B3GALNT2,THADA,NRG2,SDK1,MDM4,ELL2,ZDHHC7,RAPGEF1,CTSK,AGBL4,PDZD8,IL16,HDAC4,EXT1,ACTN4,EPN2,ARPP19,C16orf45,FCGR2A,ENO3,SUSD6,ZNF699,GDF5,RBPMS,RASGRP1,ITGA2,HNRNPM,SIPA1L3,RMND1,PPP1R2,ARL6IP4,CTSZ,PTPN18,LGR5,INPP5F,IL1B,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,SRGAP3,PTPN1,B4GALT7,AAK1,BEST1,LIMK1,CDK5RAP3,FBXL2,RAB3B,EHMT1,ZXDC,ABAT,ANO6,IKZF2,STOML1,POMGNT1,TSPAN2,CD81,FBF1,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,RALY,ZNF175,LCP1,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,RNF43,EHBP1,HPS4,CHCHD3,VEPH1,CLEC4C,FBXL13,IP6K2,GRB2,FOXN3,TAOK2,MCPH1,POC1A,LAX1,KLF13,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ERP29,ADAM19,PCCA,TBL2,STT3A,KIAA0040,CDX1,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,NINJ1,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,MTA2,PADI2,KCNIP2,RASGRF2,SIL1,LSM14A,INSC,ATP1A4,LGALS12,GDPD5,MYO9B,MYLK4,DNAJC18,SUPT3H,PPP2R5C,RNF24,CD4,DNAH2,CEACAM1,TLE4,TTC17,USPL1,DNMT3A,MACF1,TYW1B,SRF,ZBTB34,TMED10,LGR6,PDE9A,AACS,SVOPL,P4HB,MICAL1,MRPS27,TUBGCP2,TRPV6,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,FNDC3B,GUCD1,MTFR1,ODC1,FBXO34,YWHAQ,CSDE1,COLQ,IQCE,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,SHF,ADD1,IL1RN,PLEKHA7,SLC39A2,ZBTB42,DNAJC6,ACO1,WDR46,GABARAPL1,SHBG,MAPKAPK3,CHD9,SLC7A14,ANKRD35,HECW2,UGT1A8,UGGT1,EXD2,SMG5,SF3A1,SARNP,TESK2,ATG7,ACSF2,SCAF11,RHOH,SRC,PCBP2,SLC13A2,SACS,MTHFD2,PAG1,CRTC3,TAS2R5,PDE4D,SPI1,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,CCBL1,DDX56,DHX15,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,ARHGAP24,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,EPC1,PPP2R5E,RFC3,TRIM16,MARK3,NACC2,BBS1,DLGAP1,RASSF5,ATXN1,TMEM41A,ARID5B,CLTCL1,HDAC9,TMCC2,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,MBNL2,MCCC2,KCNA2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,SIN3A,STIM2,KIF26A,C7orf50,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,OXER1,BCL9,CHMP1A,FAIM2,VDR,SLX4IP,RAD21,CEBPE,CFAP45,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,SKI,KCNE1,PPM1A,HIF1A,SAG,SLC14A2,DOCK2,ILKAP,EIF4EBP1,EEF2K,TRPM4,NCOA7,ASH2L,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,PDE4DIP,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,SNCAIP,HMGXB4,SLMAP,PTP4A2,AGPS,KIAA0100,LDLRAD3,PQLC2,ST3GAL2,BICD1,LSM3,TCF7L2,CDC42BPB,ORAI2,AHCYL2,LHPP,TXNRD2,MUC20,TMEM220,PSMC1,MCC,MTURN,LSM2,ZBTB12,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,RPRD1A,CFAP43,EFHD2,RFX2,PSMD6,SPIDR,IFI35,MAP3K14,BANK1,SART1,WDR70,MEGF10,ZC3H7B,SLC25A3,PLAGL1,ICAM3,AP1M1,SLC2A5,ITGB3,TMEM51,TRAPPC10,TOP1,AGO2,CNOT10,EXOSC4,LONRF2,NR1H3,GZF1,MTA3,NIN,GOLGA3,TINAGL1,HNRNPLL,ARRDC2,ANXA9,WDR8,TMEM241,CLCN1,MED15,CARD11,RYR1,RASSF4,MAK16,GAPVD1,EPB41L2,POLR1C,GSE1,GNAI1,NR3C1,NAA25,SMIM22,SCOC,ZNF563,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,NOV,CCDC50,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,SLC39A7,TOR2A,EPHX4,NT5E,ZRANB1,OSBPL6,TRIM71,SLC39A3,SRPK1,RBM14,AGER,ETV6,YEATS2,VPS52,E2F7,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,FBXW11,OLFML2A,MIEF2,LOXL1,OGDH,CTDSPL,PAM16,NUP93,ADGRV1,TRIM26,SLC22A23,SPPL3,EYA3,PROCA1,SDCCAG8,PLA2G6,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,REV1,PEBP4,DYRK2,RXRB,HNF1B,PLEKHA6,APOL3,LDB2,SPATA24,DMXL1,ATXN7L1,STAT4,TRAF1,F5,MAPK1,KLHL29,USP39,TTC23,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,SFMBT1,PIGV,BAZ1A,TMEM123,PHF1,HSD17B12,SIRPG,PMM1,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,RANBP3,ARAP1,POLR1A,N4BP2L2,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,NOTCH2,SEPHS1,CYB5R3,SMURF2,ADGRG6,EPHX1,SHMT2,VANGL1,ADRBK2,CCL23,CRYBB1,PELI1,LIMD1,CHST15,HCN3,SPIRE1,RAB7A,TCF7,FMNL1,SPTBN2,SCN4A,ARHGAP10,HLCS,ECT2L,PEX2,FARP2,STX2,KLHDC7A,L3MBTL1,KRT2,NAA16,EPS8L3,BHLHE40,GPD1,TXNDC11,PIWIL2,SETMAR,FYN,RBKS,UPF1,ADAP1,THEMIS2,ABTB2,ANKRD11,SPOP,LRIT3,HADH,FAM83A,PPP3R1,STK10,KIF6,GID8,MSH4,ZC3H7A,RNF13,EPAS1,PER2,ASAP2,WWC2,ERMN,PROK1,ARL6IP6,TMEM63A,TRIM29,EIF1AD,PCGF3,PIK3CB,GNS,SPECC1,NAT9,PPP2R5B,RAB19,CLMN,STAT3,SLAMF1,MEF2C,MAP4K5,PYCR1,BUD13,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,TMEM17,TIGD1,CXCR4,TMEM201,DAZAP1,PGM1,IMMT,SIGLEC10,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,PEX11G,CACNB2,COL4A3BP,TAF6,NPPA,MAP4,DNAH3,ARHGAP12,RMDN3,ARFGEF2,MAP3K8,VEGFA,EME1,LRCH1,UQCRH,CPA1,ADAM12,MN1,LCLAT1,FTL,PRDM16,CPEB3,CDK14,TMEM203,FAM102A,APP,GPSM1,PRIM2,THAP4,YARS,SUSD4,RASSF1,IGF2BP2,SENP7,CRB1,AUTS2,XPO6,RUNX3,PDXDC1,CLK2,ZFYVE21,LAPTM4A,HBZ,RALGPS1,SRP68,DBNL,ADORA1,MAST2,PHF21A,CRTAM,ZBTB16,SYK,C1orf174,MAPKAP1,ADIPOR2,TIMP2,RFFL,RIOK2,OR6B1,NTRK1,CDK2,CYSTM1,CHPT1,C22orf15,RPS6KA4,ECHDC1,GPR107,ANXA2,PPARA,GTPBP2,EIF3M,GNB1,KRT71,FGF1,JMJD1C,AGL,ELOVL6,SIK2,DHRS9,JSRP1,SNX10,SHCBP1L,SGK2,ANTXR2,YWHAE,PHACTR2,KAZN,WDR1,SLA,AKT3,JAZF1,SEMA4A,SDC1,DNAJB13,PTH2R,TLE1,OLA1,CACFD1,GSAP,SLC12A6,GNAI2,YES1,EXOC6B,TSPAN33,ITGA2B,EREG,AEBP1,TMPRSS9,GPC5,SMPD3,CORO7-PAM16,MLLT1,PHACTR3,CPSF6,CREM,GRHL1,SIAH1,ACVR1B,SPAST,CALD1,PTK2,C15orf48,MBD5,AMBRA1,SLC4A1,HDAC11,ERN1,CCDC12,BASP1,RBPJ,RHOA,ESYT3,ARHGEF3,C2CD3,DOCK4,APBB1IP,TOLLIP,IKBKB,TPPP3,FER,FANCA,PDE6B,EBF3,SNUPN,DRC7,CHID1,SETBP1,MRPL10,CAPN10,ZCCHC14,STUB1,RDH5,CYTL1,CAPZA2,PHC3,CCDC167,KAT5,CEP85,SIPA1L2,SETD2,SDK2,TALDO1,CD160,MFSD10,DEDD,FOXO3,CAPN7,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,FBXO36,BSCL2,FSCN3,CDCA7,PARN,COL1A1,ATF7,SEC23B,TRAPPC3,UCKL1,FAM118A,TGFBRAP1,DHRS7,IRF2,TIMM22,GSK3B,YWHAZ,SERGEF,SLC38A6,GMEB1,DGCR2,TREM1,EMILIN2,MAPKAPK2,ORC1,RHOBTB3,CHD7,TJP3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,C16orf58,PAX8,DPP9,CPNE2,SUCNR1,MPV17,PALD1,NME2,VTI1B,MRAP,NPM3,SMCO4,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SARM1,CSRNP2,SHE,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,SIGLEC7,ATP1A1,CTLA4,FAH,TAGAP,UBXN7,MYB,ANKRD61,CYP4F12,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,PLEKHG6,KLHL3,IGF2R,CRTC1,UBR1,PHC1,GCNT2,KRT1,LRCH4,NET1,MAPRE2,NEK7,C10orf88,FARP1,PBRM1,STAMBPL1,AMFR,ACSF3,RAB25,CNNM3,RCOR1,RAD51B,CCL26,UBA7,MCF2L,MYO10,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,HOXA3,RXRA,NOD1,TAOK3,ADGRA3,ACADL,NME7,PARD3B,MYO1H,ZMYND10,EPSTI1,PNRC1,ZDHHC1,PRKG2,CSNK1G3,FAM110B,KHDRBS3,DAPP1,ZNF438,SCARF2,XPC,GNA13,ABCG8,MYOM1,HNF4A,ISM2,KANK1,WNT3A,TTC28,UBAP1,KRT6B,ZFAND2A,NR6A1,CXXC5,FNBP1,RBMS1,TAF15,CERK,STX16,DNMT1,TYSND1,MAFF,WEE1,FCRL3,PPCDC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ZFHX3,REPS1,ALDH3B1,PBX1,ATP8B1,SHROOM3,CCR3,UNC79,KIF21B,VEZF1,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CCDC86,RPL36AL,CAMTA1,PIGS,NOL10,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,SPATA25,SP110,TP53BP1,ANGPT1,ASPSCR1,PRKCA,RCC1,GLRX5,ABHD8,MDFIC,CCND3,FTO,MARK2,ATP10B,CLPB,LCORL,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,BTBD9,UPF3A,FXYD1,RELL1,GET4,SETD5,NFASC,GRK5,TBC1D14,RASAL2,COG7,NDUFV2,EFNA5,CDH15,AGPAT3,SHB,HPS1,ATP8B2,STX17,SPRED3,CNPY3,XPNPEP3,SORBS2,PDZRN3,ANKRD10,DCTN2,CXCR6,TPST2,SHPRH,PILRA,BATF,GEMIN5,RDM1,RAPGEF5,MYO1A,SLC39A1,RHBDD1,FAM207A,ADAM9,FDFT1,PARP4,GLE1,METTL9,GSTM4,NSMCE2,KDM4C,NEK6,CREB5,UBE2QL1,BRCA1,ITGB5,MNDA,BTBD11,SERPINB6,TTLL4,HPCAL1,C4orf45,NLRX1,PSMB7,SGK1,RAB11FIP3,PPRC1,NRROS,CPSF1,STXBP2,OSBPL8,STAT5B,RRP9,RNF138,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,ITGA11,SMG9,SP2,RGL1,LIG3,NCAM2,SORL1,RSU1,NFE2,DCTN5,MFSD12,TAF5L,ITGB7,ALPL,LHFPL2,CTDSPL2,FNTB,TET2,ZKSCAN3,AOAH,CRYM,NDUFA4,ATP6V0A2,CCDC183,PIEZO1,SYCE2,SAMD8,MT2A,SMYD4,HIBADH,MX1,TRAK2,CKS2,FURIN,WWP1,GTF2F2,MRC2,SLC25A13,UGT1A7,SNTB1,SLC38A11,RAB7L1,FRYL,DRAP1,ARPC4,SLC13A4,SLC16A3,KRT31,RPA1,RBM44,TEC,FANCC,SMAD5,ANXA4,SIRPA,TOX,KMT2D,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,KLRD1,PEX11A,INPP1,ECM2,ACSL6,STARD10,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,SPOCK1,UBE2K,SCAND1,EVI5L,TGFBR2,TULP4,CD82,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,GNA14,NUSAP1,GJA4,ZFC3H1,EHD4,PTPRF,LMO4,LEPROTL1,ITPR2,SLC38A1,EXOC4,TG,MYEOV,FEM1C,DCUN1D1,ZBTB7A,USP46,DHRS4,MYO5A,FBN1,RET,DUS2,TCF4,RNF11,ZNF827,CHCHD6,ZNF710,DNAJA3,ARHGEF4,MDM1,CCAR1,FAM81B,ANP32B,LRP1B,ANKRD44,EDRF1,BCL7B,TMEM130,ASL,SHANK2,NFIL3,THRSP,EEPD1,DLK1,ZBTB20,ATAD5,MKNK1,IRF7,MAT2B,HSPG2,C11orf48,PRIMPOL,BNIP3L,ATP6V1H,ARID2,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,IL18R1,KIF13B,SLC16A10,STK24,ENPP2,CCDC74B,ANKRD6,FLT3,WDR37,PM20D2,LRP4,SLC30A1,ALKBH2,GLUL,TTC22,ANKS6,MATN1,AKIRIN1,ETV3,TRAPPC12,DHX8,SLC8B1,NRXN3,VRK1,PARP16,KCNE2,EDARADD,RSPRY1,NLK,FSTL4,PRKCQ,C11orf68,TGM7,KDM6B,TNFAIP1,RCSD1,PPIC,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,LUZP6,HIF1AN,BAG2,KIF5B,LMO2,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,ITGB6,LGR4,CSF3R,CABLES1,SCAF8,IL18RAP,BUD31,UTRN,RFC4,ATP2A2,STK11IP,MDN1,AKT2,ARMC4,PRDX3,MAP4K1,KLRK1,MPL,DCP2,SIN3B,HRK,C6orf89,TBL1XR1,OSGIN1,PARP10,ZNF131,MCFD2,CCDC141,NEIL2,FGF18,CD58,CRIM1,SNRNP70,TRIM2,ZNF552,RTP2,TRAM2,FNIP1,TP53BP2,ADAMTS7,LAPTM4B,FAM91A1,MOB1A,PIAS1,IVNS1ABP,JDP2,RALGPS2,NRXN2,ZSCAN12,SRSF7,RAB3IL1,ZBTB17,PARP1,NCAPD2,TTBK2,ZBTB38,CYBRD1,NTAN1,FARS2,MEGF11,MFF,LRRC42,SPPL2B,ITGB4,TRPM7,CDH18,TMEM79,ARMC9,PRDM2,WFDC5,CAT,OSBPL10,FBXW7,MERTK,HNF1A,PSMD1,SCG3,CDC25C,RAD52,MTSS1,ADAM11,PLXNC1,NR1I2,LRFN1,RUNX1,UBASH3A,SNX4,TACR2,CRLF3,ZC3H12C,SGIP1,STAT6,SNX30,FNBP4,CTDSP2,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,HPSE2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SPSB4,SEL1L3,HS6ST1,NECAB1,EZR,AHI1,CPB1,CTSS,GABRR2,STARD3,DUT,GNPNAT1,CCDC96,SPATA16,ARHGEF10L,LRRFIP2,HYAL2,ATG16L1,CMTM7,ICA1,MTA1,PADI6,CLTC,IFFO1,CKLF,KIF13A,BBX,TNIP2,RFTN2,MYLIP,SPEF1,RPGRIP1,MAMDC2,SLC11A2,DENND1B,NDUFB9,LYN,CENPJ,AKAP2,SERBP1,GAS2L1,AKT1,ACR,GRAMD4,UBTD2,TBC1D31,UBXN1,UNC50,KPNA4,SLC1A3,ASXL1,TSPAN31,KCNA10,IL1RAP,ATXN7,PHF2,PEX14,PDE4C,RRS1,MAPK6,DOK4,MOSPD3,TFB1M,GPR39,METTL1,LTC4S,CASKIN2,PPTC7,CARD14,ALS2,DTNA,INPP5D,RAPGEF3,NR2F6,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CUEDC1,CLCC1,ZGPAT,NCOA2,ACTB,TOP2B,ORAI3,CLEC17A,BAIAP2,TNFRSF9,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,PDIK1L,WT1,SMPDL3A,ATG10,COPA,ARHGAP9,FBXW4,DNAJC5,CEP83,TSNAXIP1,CSNK1G2,RPS15A,ASB2,CLEC12A,DST,MORF4L1,CLSTN1,PSMG1,ANKRD13B,EPHA10,PCNA,DHRS11,LETM1,UBE2E2,PHB2,TLK1,PDLIM2,BUB3,NACC1,LITAF,MYO1F,TMEM19,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,ETV7,SEC24A,PSPN,DIXDC1,TNFRSF10B,MDGA1,SFI1,LIPC,KDM2B,HCLS1,ERN2,MAP2K6,CREB3L1,ODF1,FBXO9,GIPR,IL10RA,LRCH3,DNAJC4,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,ZNF692,ADIPOR1,RABGAP1L,PKD2,ZNF704,USP1,MSRA,C12orf43,ATL1,PAX7,ZMIZ1,GLIS1,DRD2,CD47,EFR3B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,NFIC,UHRF2,C1GALT1,PPP2CB,PEX7,ARAP3,ZNF652,PLAA,IL15,ARNT,NEURL1B,NCR2,SERPINF1,SLC25A10,TMEM45B,PGAP2,JPH2,DNAJC13,RAB27A,CREB3L3,BRD7,MIA3,TRIM62,ZP1,GMPPB,A2ML1,ARID4B,PFKFB4,CEP295,ALOX5,EHMT2,COQ5,ZBTB10,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,CGN,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,CA4,EIF4G3,SMCHD1,OAT,MGST2,DLGAP4,LRP12,FYCO1,C17orf63,MS4A6E,MICU1,SEMA3F,RBFOX2,DCTN4,EAF2,ZNF337,PEAK1,FLOT1,CAND2,SPAG4,DNASE1,YOD1,NOX3,LMNB1,CXCL3,APLF,LIMCH1,GLYCTK,THSD7A,GNA15,CNKSR3,WIZ,ELF1,TSPAN14,STAU2,NFE2L1,DGAT2,DLC1,ATXN10,ALOX12B,OTULIN,PRR5,YY1AP1,PPP2R1A,CCL28,TMEM50B,DYM,MCCC1,KPNB1,KCNN3,KRI1,CLPTM1,GPRC5A,CDH22,GALNT11,FAM149B1,CDYL,ACVR2A,DBN1,HSPD1,HMOX2,COLGALT2,TBC1D13,PWWP2A,OIT3,MAP3K4,NAPG,ALCAM,PROK2,CARS,ARMC2,RAB8B,RAP1A,TNPO1,MTF1,FGD5,RASGRP3,PSEN1,SGSM2,SMYD5,P2RY6,SOX6,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,TEX14,GRM2,PPP1CA,INTS8,SEC63,MPRIP,REEP5,ITFG2,NGLY1,GIT2,USP47,SPIRE2,KLHL5,GPS2,KLHDC4,RASSF8,ZEB1,WDR7,SEMA6D,MMP28,GMDS,C5AR2,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,SBSN,RNF19A,CPT1A,MNT,SEMA4C,GSPT1,QKI,ARL2,BTN3A3,FKBP1B,MRPS14,PWP2,BATF3,IQGAP1,CCDC112,AMPD2,AFTPH,ACIN1,TOR1B,CD6,HBS1L,ANKRD9,NCAM1,ATF6,PDPK1,MAP2K3,PLCB1,ADD3,CD84,BIK,NUCKS1,PRPF8,PACS2,ZNF19,MON2,ALAD,PANK1,CCDC146,EXTL1,RPS6KA1,NEK1,NMNAT1,KIF3B,SUFU,STX1B,CNST,GRK6,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ZZZ3,ESYT2,SLC40A1,ZFAND6,RB1CC1,SCG5,DFFA,C17orf62,PKNOX1,RCBTB2,COG2,IL2RA,RUNX2,NCLN,ST14,PAK2,ALAS1,FLT1,CLCN7,DOCK10,FBL,EMID1,PRKAR2A,ZNF740,RSPH14,PCM1,MTMR7,TRPM5,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,C1QTNF6,PCOLCE,MARK4,C9orf152,C9orf64,DHX33,SDCBP2,PIK3R3,GLRB,ASB3,JADE2,MAP3K5,MEOX1,ATP6V0D1,ZMYND8,BCAS4,DTHD1,KLHDC3,NPTN,HSPB1,SORBS1,TXNDC2,PIKFYVE,CAMK4,DDA1
## 1825 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,FBXW8,MITF,ABCC1,SLC7A1,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,OSBPL5,TRIO,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,NKIRAS2,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,ITGAE,SLC2A8,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,GNAO1,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,SSBP3,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,COTL1,CLIP1,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,TPST1,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,INPP5A,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,NSMCE1,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,WWP2,P2RY2,FADD,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ACSL1,ABR,DOCK1,NEMF,RAB11FIP1,PRKAG2,MAP1LC3B2,FHL2,DAB1,RALGDS,NUTF2,CCL18,ELMO2,SLC2A9,GJB3,SGMS1,SPATS2L,POLR2F,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,SLC41A1,FOXJ3,CLRN1,HMGCL,KLF16,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,CALML4,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,MYLK,ADTRP,TMOD3,SAP30L,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,AMZ2,ZNF70,IL13,CCNY,DMAP1,ZNF789,PRX,RREB1,ERGIC1,TMEM154,PLA2G1B,ABCC4,ADAMTS14,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,SLC12A4,PROZ,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,CATSPER4,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,MFAP4,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,TNN,PPP1R16B,NCK2,RNF157,IKZF1,HECW1,MAML1,SLC29A3,SULF2,GSTM3,TGFA,GALNT12,CEBPB,STK3,ARID1B,PTGDR2,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HTT,HPD,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,BAIAP2L1,SPTBN1,MYL9,GLB1,TNXB,DENND5A,LGALS4,HK3,XYLT1,CD86,SOAT2,FMO1,MAN1C1,METTL16,RAP1GAP2,MED12L,UNC5B,COL20A1,NEDD4L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,ZNF532,SIK3,EML3,VSIG10,ZSWIM3,SNX9,LRRN2,BCL7A,SLC43A3,MCMBP,DNAJC3,KAT8,PLA1A,WNT3,GALNT7,UXS1,MTUS2,DHCR24,CDH23,EVPL,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,CDKN2AIPNL,SERP2,WDFY2,RNF216,TBC1D10A,AGAP3,BACH2,CORO2A,EFNB2,ATG13,NEK8,CD7,LARP1,TBC1D9B,CACNA1D,KBTBD4,LRRC8C,P2RX7,SLC11A1,PIK3AP1,P3H2,C1QTNF1,VPS13D,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,AJAP1,TPM3,CCDC57,CALR3,PLLP,UBE2G1,PRKDC,DESI1,RFT1,GAS7,HK1,RIN3,SLC7A11,MLST8,JAG1,ST7,XAF1,DNHD1,ERG,IMPA2,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,HPX,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,NAV2,MAPRE3,LRRC8D,PSD3,ASB8,SMYD3,IL34,RPH3AL,NUDT1,FOCAD,DSC1,LBR,NDRG1,ADAR,ACAD10,HVCN1,SMG6,RHOBTB2,SECISBP2L,SND1,MBD6,RCC2,PAFAH2,SLIT3,USP19,ITPRIP,DCAKD,IL18BP,SREBF2,ASIC1,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,THRB,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,SEC14L2,NAPA,LEF1,OSBP2,LRRC20,FAM104A,RIBC2,HDC,PRNP,RHBDD2,C16orf70,SPATA21,IQCD,DHX30,PRDM10,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,MIDN,VEGFB,DNAH1,B3GALNT2,THADA,NRG2,SDK1,MDM4,ELL2,ZDHHC7,RAPGEF1,CTSK,AGBL4,PDZD8,IL16,HDAC4,EXT1,ACTN4,EPN2,ARPP19,GPD2,C16orf45,FCGR2A,ENO3,SUSD6,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,ITGA2,FTCDNL1,HNRNPM,SIPA1L3,RMND1,PPP1R2,ARL6IP4,CTSZ,PTPN18,LGR5,INPP5F,IL1B,AFF1,WDR73,ADCY9,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,SRGAP3,PTPN1,B4GALT7,AAK1,BEST1,LIMK1,CDK5RAP3,FBXL2,RAB3B,EHMT1,ZXDC,ABAT,ANO6,IKZF2,STOML1,POMGNT1,TSPAN2,CD81,KIAA0232,PIK3R5,FBF1,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,TOP1MT,RALY,DIDO1,ZNF175,LCP1,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,ATP2C1,RNF43,EHBP1,HPS4,CHCHD3,VEPH1,ZNFX1,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,FOXN3,TAOK2,MCPH1,POC1A,LAX1,KLF13,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ZSWIM4,ERP29,ADAM19,PCCA,TBL2,STT3A,KIAA0040,CDX1,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,NINJ1,P4HTM,DGKG,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,MTA2,PADI2,KCNIP2,RASGRF2,SIL1,LSM14A,INSC,ATP1A4,LFNG,LGALS12,GDPD5,MYO9B,MYLK4,DNAJC18,SUPT3H,PPP2R5C,ERI3,RNF24,CD4,DNAH2,CEACAM1,TLE4,TTC17,USPL1,DNMT3A,RBM33,MACF1,TYW1B,SRF,ZBTB34,TMED10,LGR6,PDE9A,AACS,SVOPL,P4HB,MICAL1,ACAD8,MRPS27,TUBGCP2,TRPV6,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,FNDC3B,GUCD1,MTFR1,ERAP2,ODC1,RAB20,FBXO34,YWHAQ,CSDE1,COLQ,IQCE,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,SHF,ADD1,IL1RN,PLEKHA7,SLC39A2,ZBTB42,DNAJC6,ACO1,WDR46,GABARAPL1,SHBG,MAPKAPK3,CHD9,SLC7A14,ANKRD35,HECW2,UGT1A8,UGGT1,EXD2,SMG5,EARS2,SF3A1,SARNP,TESK2,ATG7,ACSF2,SCAF11,RHOH,SRC,PCBP2,SLC13A2,SACS,MTHFD2,PAG1,TBXAS1,CRTC3,TAS2R5,PDE4D,SPI1,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,CCBL1,DDX56,DHX15,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,ARHGAP24,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,EPC1,PPP2R5E,RFC3,TRIM16,MARK3,NACC2,CAMP,BBS1,DLGAP1,RASSF5,ATXN1,TMEM41A,ARID5B,CLTCL1,HDAC9,TMCC2,ARFGAP2,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,MBNL2,MCCC2,KCNA2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,SIN3A,STIM2,KIF26A,C7orf50,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,OXER1,BCL9,CHMP1A,FAIM2,VDR,SLX4IP,RAD21,CEBPE,CFAP45,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,SKI,KCNE1,PPM1A,NMUR1,HIF1A,SAG,SLC14A2,DOCK2,ILKAP,TNRC18,HIVEP2,EIF4EBP1,EEF2K,TRPM4,NCOA7,ASH2L,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,PDE4DIP,CPD,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,SNCAIP,HMGXB4,SLMAP,PTP4A2,AGPS,KIAA0100,LDLRAD3,PQLC2,ST3GAL2,BICD1,LSM3,TCF7L2,CDC42BPB,ORAI2,AHCYL2,CUX1,LHPP,TXNRD2,RNF149,MUC20,TMEM220,PSMC1,MCC,MTURN,LSM2,ZBTB12,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,RPRD1A,CFAP43,EFHD2,RFX2,PSMD6,SPIDR,IFI35,MAP3K14,BANK1,SART1,WDR70,MEGF10,ZC3H7B,SLC25A3,PLAGL1,ICAM3,AP1M1,SLC2A5,ITGB3,TMEM51,TRAPPC10,TOP1,AGO2,CNOT10,EXOSC4,LONRF2,NR1H3,GZF1,MTA3,NIN,GOLGA3,TINAGL1,HNRNPLL,ARRDC2,ANXA9,WDR8,TMEM241,CLCN1,MED15,PRG3,CARD11,RYR1,RASSF4,MAK16,GAPVD1,EPB41L2,POLR1C,GSE1,GNAI1,NR3C1,NAA25,SMIM22,HAVCR1,SCOC,ZNF563,TGM3,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,NOV,CRISPLD2,CCDC50,IQSEC1,CYP3A43,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,GALNS,SLC39A7,TOR2A,EPHX4,NT5E,ZRANB1,OSBPL6,TRIM71,SLC39A3,SRPK1,BEND6,RBM14,AGER,MIR101-2,ETV6,YEATS2,VPS52,E2F7,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,FBXW11,OLFML2A,MIEF2,LOXL1,OGDH,ZZEF1,CTDSPL,PAM16,MAN1A1,RAB40C,NUP93,ADGRV1,TRIM26,SLC22A23,SPPL3,EYA3,PROCA1,SDCCAG8,PLA2G6,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,REV1,PEBP4,DYRK2,RXRB,HNF1B,PLEKHA6,DDX27,APOL3,LDB2,SPATA24,DMXL1,ATXN7L1,GALNTL6,STAT4,TRAF1,F5,MAPK1,KLHL29,USP39,TTC23,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,SFMBT1,PIGV,BAZ1A,TMEM123,SUSD1,PHF1,HSD17B12,SIRPG,PMM1,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,RANBP3,SPATA5,ARAP1,POLR1A,TUBD1,N4BP2L2,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,NOTCH2,SEPHS1,CYB5R3,SMURF2,DTD1,ADGRG6,EPHX1,SHMT2,VANGL1,ADRBK2,CCL23,ARID4A,CRYBB1,PELI1,LIMD1,CHST15,HCN3,SPIRE1,RAB7A,TCF7,FMNL1,SPTBN2,SCN4A,ARHGAP10,HLCS,ECT2L,PEX2,FARP2,STX2,KLHDC7A,L3MBTL1,IDO1,KRT2,NAA16,EPS8L3,BHLHE40,GPD1,TXNDC11,PIWIL2,CELF2,SETMAR,FYN,RBKS,UPF1,ADAP1,POLR3A,THEMIS2,ABTB2,ANKRD11,SPOP,LRIT3,TSNAX-DISC1,HADH,FAM83A,PPP3R1,STK10,LSG1,KIF6,GID8,MSH4,ZC3H7A,RNF13,EPAS1,CPM,PER2,ASAP2,WWC2,ERMN,PROK1,ARL6IP6,TMEM63A,TRIM29,EIF1AD,PCGF3,PIK3CB,GNS,SPECC1,NAT9,PPP2R5B,RAB19,CLMN,STAT3,SLAMF1,SYN3,MEF2C,MAP4K5,EEFSEC,PYCR1,BUD13,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,GRK4,TMEM17,TIGD1,CXCR4,TMEM201,DAZAP1,PGM1,IMMT,SIGLEC10,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,PEX11G,CACNB2,COL4A3BP,IDNK,TAF6,NPPA,MAP4,DNAH3,ARHGAP12,RMDN3,EFCAB5,ARFGEF2,MAP3K8,VEGFA,EME1,LRCH1,UQCRH,CPA1,ADAM12,MN1,LCLAT1,PLEKHM3,FTL,PRDM16,CPEB3,CDK14,TMEM203,FAM102A,APP,GPSM1,PRIM2,THAP4,YARS,SUSD4,RASSF1,CSAD,IGF2BP2,SENP7,CRB1,AUTS2,CHSY1,XPO6,RUNX3,PDXDC1,ZNF852,CLK2,ACOXL,ZFYVE21,LAPTM4A,HBZ,RALGPS1,SRP68,DBNL,ADORA1,PLA2G4F,MAST2,PHF21A,CRTAM,GDA,ZBTB16,SYK,C1orf174,MAPKAP1,ADIPOR2,TIMP2,RFFL,DPEP2,H6PD,AFF3,RIOK2,OR6B1,NTRK1,CDK2,CYSTM1,CHPT1,C22orf15,RPS6KA4,ECHDC1,GPR107,ANXA2,PPARA,GTPBP2,EIF3M,GNB1,KRT71,FGF1,JMJD1C,AGL,ELOVL6,SIK2,DHRS9,JSRP1,SNX10,SHCBP1L,SGK2,ANTXR2,YWHAE,SLFN14,PHACTR2,KAZN,WDR1,SLA,AKT3,JAZF1,SEMA4A,SDC1,DNAJB13,PTH2R,TLE1,PLA2G15,OLA1,CACFD1,GSAP,MIR3909,SLC12A6,GNAI2,YES1,EXOC6B,TSPAN33,ITGA2B,EREG,AEBP1,TMPRSS9,GPC5,RBM19,CPPED1,SMPD3,CORO7-PAM16,MLLT1,PHACTR3,CPSF6,CREM,GRHL1,SIAH1,ACVR1B,SPAST,ALKBH5,CALD1,PTK2,C15orf48,MBD5,AMBRA1,SLC4A1,HDAC11,ERN1,CCDC12,BASP1,RBPJ,RHOA,ESYT3,ARHGEF3,C2CD3,DOCK4,APBB1IP,TOLLIP,IKBKB,TPPP3,FER,KLF7,FANCA,PDE6B,EBF3,SNUPN,ENPP3,DRC7,CHID1,SETBP1,MRPL10,CAPN10,ZCCHC14,ULK4,STUB1,RDH5,CDK19,CYTL1,CAPZA2,PHC3,CCDC167,ENTPD7,KAT5,CEP85,SIPA1L2,SETD2,SDK2,TALDO1,CD160,MFSD10,DEDD,FOXO3,CAPN7,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,FBXO36,BSCL2,FSCN3,CDCA7,PARN,COL1A1,CLCNKB,ATF7,SEC23B,TRAPPC3,UCKL1,OTOF,FAM118A,TGFBRAP1,DHRS7,IRF2,TIMM22,GSK3B,YWHAZ,SSTR1,SERGEF,SLC38A6,GMEB1,DGCR2,TREM1,EMILIN2,ZC3H4,MAPKAPK2,ORC1,RHOBTB3,CHD7,TJP3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,C16orf58,RBM34,PAX8,DPP9,CPNE2,SUCNR1,MPV17,PALD1,ZCCHC24,CLCN6,NME2,VTI1B,MRAP,NPM3,SMCO4,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SARM1,CSRNP2,SHE,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,SIGLEC7,ATP1A1,CTLA4,FAH,TAGAP,PGD,UBXN7,MYB,ANKRD61,CYP4F12,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,PLEKHG6,KLHL3,ADK,IGF2R,CRTC1,MYT1,UBR1,PHC1,GCNT2,KRT1,LRCH4,NET1,MAPRE2,NEK7,C10orf88,FARP1,PBRM1,STAMBPL1,AMFR,ACSF3,RAB25,CNNM3,RCOR1,RAD51B,CCL26,UBA7,MCF2L,MYO10,LPCAT1,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,HOXA3,RXRA,NOD1,TAOK3,ADGRA3,ACADL,NME7,PARD3B,MYO1H,ZMYND10,EPSTI1,PNRC1,SLFNL1,ZDHHC1,PRKG2,CSNK1G3,FAM110B,KHDRBS3,DAPP1,ZNF438,EDEM2,SCARF2,XPC,GNA13,ABCG8,ALDH1A2,MYOM1,HNF4A,ISM2,KANK1,WNT3A,TTC28,UBAP1,KRT6B,ZFAND2A,NR6A1,CXXC5,RNF121,SCTR,FNBP1,RBMS1,TAF15,CERK,STX16,DNMT1,TYSND1,MAFF,WEE1,FCRL3,NUGGC,PPCDC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ZFHX3,REPS1,ALDH3B1,PBX1,ATP8B1,SHROOM3,CCR3,UNC79,KIF21B,VEZF1,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CNGA4,CCDC86,ADCK1,GDPD3,RPL36AL,TTL,CAMTA1,PIGS,NOL10,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,SPATA25,SP110,TP53BP1,ANGPT1,ASPSCR1,C14orf43,PRKCA,RCC1,GLRX5,ABHD8,MDFIC,CCND3,FTO,MARK2,ATP10B,GPR183,CLPB,LCORL,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,BTBD9,UPF3A,FXYD1,RELL1,GET4,SETD5,NFASC,GRK5,TBC1D14,CUX2,RASAL2,COG7,TEX2,NDUFV2,EFNA5,CDH15,ZNF865,AGPAT3,SHB,HPS1,ATP8B2,STX17,SPRED3,CNPY3,XPNPEP3,SORBS2,PDZRN3,ANKRD10,DCTN2,CXCR6,TPST2,SHPRH,PILRA,BATF,GEMIN5,RDM1,RAPGEF5,MYO1A,SLC39A1,RHBDD1,FAM207A,ADAM9,FDFT1,PARP4,GLE1,METTL9,GSTM4,NSMCE2,KDM4C,NEK6,CREB5,UBE2QL1,BRCA1,ITGB5,MNDA,ZNF507,BTBD11,SERPINB6,TTLL4,HPCAL1,C4orf45,NLRX1,PSMB7,SGK1,RAB11FIP3,PPRC1,ACSM6,NRROS,CPSF1,STXBP2,OSBPL8,STAT5B,RRP9,RNF138,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,ITGA11,SMG9,SP2,RGL1,LIG3,NCAM2,SORL1,TRPM2,RSU1,NFE2,DCTN5,MFSD12,TAF5L,ITGB7,ALPL,LHFPL2,CTDSPL2,FNTB,TET2,ZKSCAN3,AOAH,CRYM,NDUFA4,ATP6V0A2,CCDC183,PIEZO1,SYCE2,ALPK3,SAMD8,MT2A,SMYD4,HIBADH,MX1,TRAK2,CKS2,FURIN,UNK,YDJC,WWP1,GTF2F2,MRC2,SLC25A13,UGT1A7,SNTB1,SLC38A11,RAB7L1,FRYL,DRAP1,ARPC4,LTB4R,SLC13A4,SLC16A3,KRT31,RPA1,RBM44,TEC,FANCC,HCRTR1,SMAD5,ANXA4,SIRPA,TOX,KMT2D,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,KLRD1,BAHCC1,PEX11A,INPP1,ECM2,ACSL6,STARD10,POPDC2,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,SPOCK1,UBE2K,SCAND1,EVI5L,TGFBR2,TULP4,CD82,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,PPM1L,ZNF215,GNA14,NUSAP1,GJA4,ZFC3H1,EHD4,PTPRF,LMO4,LEPROTL1,ITPR2,SLC38A1,EXOC4,TG,MYEOV,FEM1C,RNF145,DCUN1D1,ZBTB7A,USP46,DHRS4,MYO5A,FBN1,RET,DUS2,TCF4,RNF11,ZNF827,CHCHD6,ZNF710,DNAJA3,ARHGEF4,MDM1,CCAR1,REXO2,FAM81B,ARHGAP35,ANP32B,LRP1B,ANKRD44,EDRF1,BCL7B,TMEM130,ASL,SHANK2,NFIL3,THRSP,EEPD1,DLK1,ZBTB20,ATAD5,MKNK1,IRF7,MAT2B,HSPG2,C11orf48,PRIMPOL,BNIP3L,ATP6V1H,ARID2,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,IL18R1,KIF13B,SLC16A10,STK24,ENPP2,CCDC74B,ANKRD6,FLT3,WDR37,PM20D2,LRP4,ZNF638,SLC30A1,ALKBH2,RRBP1,GLUL,TTC22,ANKS6,MATN1,AKIRIN1,PDE7A,ETV3,TRAPPC12,SLC27A3,DHX8,SLC8B1,APOLD1,NRXN3,VRK1,PARP16,KCNE2,EDARADD,RSPRY1,NLK,FSTL4,PRKCQ,C11orf68,TGM7,KDM6B,TNFAIP1,RCSD1,CERKL,PPIC,TLL2,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,LUZP6,HIF1AN,BAG2,KIF5B,LMO2,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,ITGB6,LGR4,CSF3R,CABLES1,SCAF8,DCLK3,PRPF38B,IL18RAP,BUD31,UTRN,RFC4,ATP2A2,STK11IP,MDN1,AKT2,ARMC4,PRDX3,MAP4K1,KLRK1,MPL,DCP2,SIN3B,HRK,C6orf89,TBL1XR1,OSGIN1,PARP10,ZNF131,MCFD2,URGCP,CCDC141,NEIL2,FGF18,CD58,CRIM1,SNRNP70,TRIM2,ZNF552,RTP2,TRAM2,FNIP1,TP53BP2,ADAMTS7,LAPTM4B,FAM91A1,MOB1A,PIAS1,CLYBL,IVNS1ABP,JDP2,RALGPS2,ARSK,NRXN2,ZSCAN12,SRSF7,RAB3IL1,ZBTB17,PARP1,NCAPD2,TTBK2,ZBTB38,CYBRD1,NTAN1,FARS2,MEGF11,MFF,LRRC42,SPPL2B,ITGB4,TRPM7,CDH18,TMEM79,ARMC9,PRDM2,WFDC5,CAT,OSBPL10,FBXW7,MERTK,LILRA1,HNF1A,PSMD1,SCG3,CDC25C,RAD52,MTSS1,ADAM11,PLXNC1,NR1I2,LRFN1,RUNX1,UBASH3A,SNX4,TACR2,ZSCAN25,CRLF3,ZC3H12C,SGIP1,STAT6,SNX30,FNBP4,CTDSP2,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,HPSE2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SPSB4,SEL1L3,HS6ST1,NECAB1,EZR,AHI1,CPB1,CTSS,GABRR2,STARD3,DUT,GNPNAT1,CCDC96,SPATA16,RNF130,ARHGEF10L,LRRFIP2,ZNF333,PLA2G4A,HYAL2,CA12,ATG16L1,CMTM7,ICA1,MTA1,PADI6,CLTC,IFFO1,CKLF,KIF13A,BBX,TNIP2,RFTN2,MYLIP,SPEF1,RPGRIP1,MAMDC2,SLC11A2,DENND1B,NDUFB9,LYN,CENPJ,AKAP2,SERBP1,GAS2L1,AKT1,ACR,GRAMD4,UBTD2,TBC1D31,UBXN1,UNC50,KPNA4,SLC1A3,ASXL1,TSPAN31,KCNA10,IL1RAP,ATXN7,PHF2,PEX14,PDE4C,ALPK2,RRS1,MAPK6,DOK4,MOSPD3,TFB1M,GPR39,ZADH2,HIPK3,METTL1,LTC4S,CASKIN2,PPTC7,CARD14,ALS2,DTNA,ZNRF2,INPP5D,RAPGEF3,NR2F6,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CUEDC1,CLCC1,A3GALT2,ZGPAT,NCOA2,ACTB,TOP2B,ORAI3,CLEC17A,BAIAP2,TNFRSF9,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,PDIK1L,WT1,SMPDL3A,ATG10,COPA,ARHGAP9,FBXW4,DNAJC5,CEP83,TSNAXIP1,CSNK1G2,RPS15A,ASB2,CLEC12A,DST,MORF4L1,CLSTN1,PSMG1,ANKRD13B,EPHA10,PCNA,DHRS11,LETM1,UBE2E2,PHB2,TLK1,PDLIM2,BUB3,NACC1,LITAF,MYO1F,TMEM19,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,ETV7,SEC24A,PSPN,DIXDC1,TNFRSF10B,MDGA1,SFI1,LIPC,KDM2B,HCLS1,ERN2,MAP2K6,CREB3L1,ODF1,FBXO9,GIPR,IL10RA,LRCH3,DNAJC4,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,ZNF692,ADIPOR1,RABGAP1L,PKD2,ZNF704,USP1,NARS2,MSRA,C12orf43,ATL1,PAX7,ZMIZ1,GLIS1,DRD2,CD47,EFR3B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,NFIC,UHRF2,C1GALT1,PPP2CB,PEX7,ARAP3,ZNF652,PLAA,IL15,ARNT,NEURL1B,NCR2,SERPINF1,SLC25A10,TMEM45B,CPA3,PGAP2,JPH2,DNAJC13,RAB27A,CREB3L3,BRD7,ATAD3C,MIA3,TRIM62,ZP1,GMPPB,A2ML1,ARID4B,PFKFB4,CEP295,ALOX5,EHMT2,COQ5,ZBTB10,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,CGN,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,CA4,EIF4G3,SMCHD1,OAT,MGST2,DLGAP4,LRP12,FYCO1,C17orf63,MGAM2,MS4A6E,MICU1,SEMA3F,RBFOX2,DCTN4,EAF2,ZNF337,PEAK1,FLOT1,CAND2,SPAG4,DNASE1,YOD1,NOX3,LMNB1,CXCL3,APLF,LIMCH1,GLYCTK,THSD7A,GNA15,CNKSR3,LOC81691,WIZ,ELF1,TSPAN14,STAU2,NFE2L1,DGAT2,DLC1,ATXN10,ALOX12B,MYRFL,OTULIN,PRR5,YY1AP1,PPP2R1A,CCL28,TMEM50B,DYM,MCCC1,KPNB1,KCNN3,KRI1,CLPTM1,NUDT19,GPRC5A,CDH22,ALDH6A1,GALNT11,FAM149B1,CDYL,ACVR2A,RNF224,DBN1,HSPD1,HMOX2,COLGALT2,HIVEP3,TBC1D13,PWWP2A,OIT3,MAP3K4,NAPG,ALCAM,EDEM3,PROK2,CARS,ARMC2,RAB8B,RAP1A,TNPO1,MTF1,FGD5,RASGRP3,PSEN1,MRPL16,SGSM2,SMYD5,P2RY6,FER1L6,SOX6,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,TEX14,GRM2,PPP1CA,INTS8,SEC63,FDX1,MPRIP,REEP5,ITFG2,NGLY1,GIT2,USP47,SPIRE2,ZNF516,SPTLC2,KLHL5,GPS2,KLHDC4,RASSF8,ZEB1,WDR7,SEMA6D,MMP28,GMDS,PGS1,C5AR2,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,SBSN,RNF19A,CPT1A,MNT,SEMA4C,GSPT1,QKI,ARL2,BTN3A3,FKBP1B,MRPS14,PWP2,BATF3,IQGAP1,CCDC112,AMPD2,AFTPH,ACIN1,TOR1B,CD6,HBS1L,ANKRD9,NCAM1,ATF6,PDPK1,MAP2K3,PLCB1,GALNT18,ADD3,CD84,BIK,NUCKS1,PRPF8,PACS2,ZNF19,MON2,ALAD,PANK1,CCDC146,EXTL1,RPS6KA1,NEK1,NMNAT1,KIF3B,SUFU,STX1B,CNST,GRK6,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ZZZ3,TGIF2,ESYT2,SLC40A1,GALK2,ZFAND6,RASA2,RB1CC1,SCG5,DFFA,C17orf62,PKNOX1,RCBTB2,COG2,IL2RA,RUNX2,NCLN,ST14,PAK2,ALAS1,FLT1,CLCN7,DOCK10,FBL,EMID1,ZNF565,PRKAR2A,ZNF740,RSPH14,PCM1,RNASET2,MTMR7,TRPM5,ZNF518B,ZFAT,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,C1QTNF6,PCOLCE,MARK4,C9orf152,C9orf64,DHX33,SDCBP2,PIK3R3,GLRB,ASB3,JADE2,MAP3K5,MEOX1,ATP6V0D1,ZMYND8,BCAS4,DTHD1,KLHDC3,NPTN,HSPB1,SORBS1,TXNDC2,PIKFYVE,CAMK4,DDA1
## 1826 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,SLC29A1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,GPR176,FBXW8,MITF,SLC25A33,ABCC1,SLC7A1,SLC4A5,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,OSBPL5,TRIO,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,NKIRAS2,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,ITGAE,SLC2A8,GATAD2A,HMBS,TTC38,NDST2,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,SLC24A3,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,TTYH3,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,SLC45A4,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,GNAO1,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,SSBP3,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,SLC39A4,TPST1,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,INPP5A,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,ADORA3,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,NSMCE1,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,PNPLA1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,WWP2,P2RY2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ACSL1,ABR,DOCK1,NEMF,RAB11FIP1,SPNS3,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,RALGDS,NUTF2,CCL18,ELMO2,COL15A1,SLC2A9,GJB3,SGMS1,SPATS2L,POLR2F,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,SLC41A1,FOXJ3,CLRN1,HMGCL,KLF16,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,GPR156,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,CALML4,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,MYLK,ADTRP,TMOD3,SAP30L,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,AMZ2,ZNF70,IL13,CCNY,DMAP1,ZNF789,SLC23A2,PRX,RREB1,ERGIC1,TMEM154,PLA2G1B,ABCC4,ADAMTS14,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,SLC12A4,PROZ,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,CATSPER4,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,MFAP4,CCDC182,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,TNN,PPP1R16B,NCK2,ST3GAL4,RNF157,IKZF1,HECW1,MAML1,SLC29A3,SULF2,GSTM3,TGFA,GALNT12,CEBPB,STK3,ARID1B,PTGDR2,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HTT,HPD,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,BAIAP2L1,SPTBN1,MYL9,GLB1,TNXB,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,CD86,SOAT2,FMO1,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,UNC5B,COL20A1,NEDD4L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,SOGA1,ZNF532,SIK3,EML3,VSIG10,ZSWIM3,SNX9,LRRN2,BCL7A,SLC43A3,MCMBP,DNAJC3,KAT8,PLA1A,WNT3,GALNT7,UXS1,MTUS2,DHCR24,CDH23,EVPL,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,TMEM116,ELL3,NFATC2,ZHX2,TMEM104,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,PIGN,CDKN2AIPNL,SERP2,WDFY2,RNF216,TBC1D10A,AGAP3,BACH2,CORO2A,EFNB2,ATG13,NEK8,CD7,LARP1,TBC1D9B,CACNA1D,KBTBD4,CHRNE,LRRC8C,P2RX7,SLC11A1,PIK3AP1,P3H2,C1QTNF1,VPS13D,OSBPL3,ASNSD1,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,AJAP1,TPM3,CCDC57,CALR3,PLLP,UBE2G1,PRKDC,DESI1,RFT1,GAS7,MBTPS1,HK1,RIN3,SLC7A11,MLST8,JAG1,ST7,XAF1,DNHD1,ERG,IMPA2,ACRBP,VAMP1,AGXT,NAP1L4,PIGL,NPL,GTPBP1,HPX,CLDN10,VGLL4,GTSF1L,GON4L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,NAV2,MAPRE3,LRRC8D,PSD3,ASB8,ZDHHC18,SMYD3,IL34,RPH3AL,NUDT1,FOCAD,DSC1,LBR,NDRG1,ADAR,ACAD10,HVCN1,SMG6,RHOBTB2,SECISBP2L,SND1,MBD6,RCC2,PAFAH2,SLC45A3,SLIT3,USP19,ITPRIP,DCAKD,IL18BP,SREBF2,ASIC1,TMIGD3,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,THRB,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,SEC14L2,NAPA,LEF1,OSBP2,LRRC20,FAM104A,RIBC2,HDC,PRNP,RHBDD2,C16orf70,SPATA21,IQCD,DHX30,PRDM10,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,MIDN,VEGFB,DNAH1,B3GALNT2,HNMT,THADA,NRG2,SDK1,MDM4,ELL2,ZDHHC7,RAPGEF1,CTSK,AGBL4,PDZD8,IL16,HDAC4,EXT1,ACTN4,EPN2,ARPP19,GPD2,C16orf45,FCGR2A,ENO3,SUSD6,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,ITGA2,FTCDNL1,HNRNPM,SIPA1L3,RMND1,PPP1R2,ARL6IP4,CTSZ,PTPN18,LGR5,INPP5F,IL1B,AFF1,WDR73,ADCY9,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,SRGAP3,PTPN1,B4GALT7,AAK1,BEST1,LIMK1,CDK5RAP3,FBXL2,RAB3B,EHMT1,ZXDC,ABAT,ANO6,IKZF2,STOML1,POMGNT1,TSPAN2,CD81,KIAA0232,PIK3R5,FBF1,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,TOP1MT,RALY,DIDO1,ZNF175,LCP1,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,SLC7A7,ATP2C1,RNF43,EHBP1,HPS4,CHCHD3,VEPH1,ZNFX1,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,EMC1,FOXN3,TAOK2,MCPH1,POC1A,LAX1,GPR35,KLF13,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ZSWIM4,ERP29,ADAM19,PCCA,TBL2,STT3A,KIAA0040,CDX1,DHX37,MVB12A,CLK3,TBC1D2,CPVL,KCNAB2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,NINJ1,CHST11,P4HTM,DGKG,MBOAT1,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,MTA2,PLD5,PADI2,KCNIP2,RASGRF2,SIL1,LSM14A,INSC,ATP1A4,LFNG,LGALS12,GDPD5,MYO9B,MYLK4,DNAJC18,SUPT3H,PPP2R5C,ERI3,SLC35D1,RNF24,CD4,DNAH2,CEACAM1,TLE4,TTC17,USPL1,DNMT3A,RBM33,MACF1,TYW1B,SRF,ZBTB34,TMED10,LGR6,PDE9A,AACS,SVOPL,P4HB,MICAL1,ACAD8,MRPS27,TUBGCP2,TRPV6,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,FNDC3B,GUCD1,MTFR1,ERAP2,ODC1,RAB20,FBXO34,YWHAQ,CSDE1,COLQ,IQCE,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,SHF,ADD1,IL1RN,PLEKHA7,SLC39A2,ZBTB42,DNAJC6,ACO1,WDR46,GABARAPL1,SHBG,MAPKAPK3,CHD9,SLC7A14,ANKRD35,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SF3A1,SARNP,TESK2,ATG7,ACSF2,SCAF11,RHOH,SRC,PCBP2,SLC13A2,SACS,MTHFD2,PAG1,TBXAS1,CRTC3,TAS2R5,PDE4D,SPI1,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,CCBL1,DDX56,DHX15,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,ARHGAP24,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,EPC1,PPP2R5E,RFC3,TRIM16,MARK3,NACC2,CAMP,BBS1,DLGAP1,RASSF5,ATXN1,TMEM41A,ARID5B,CLTCL1,HDAC9,SLC44A4,TMCC2,ARFGAP2,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,SLC25A45,MBNL2,MCCC2,KCNA2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,SIN3A,STIM2,KIF26A,C7orf50,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,OXER1,BCL9,CHMP1A,FAIM2,VDR,SLX4IP,RAD21,CEBPE,CFAP45,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,DEPDC1B,SKI,KCNE1,PPM1A,NMUR1,HIF1A,SAG,SLC14A2,DOCK2,ILKAP,TNRC18,HIVEP2,EIF4EBP1,RGS9,EEF2K,TRPM4,TMEM131,NCOA7,ASH2L,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,ART3,PDE4DIP,CPD,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,SNCAIP,HMGXB4,SLMAP,PTP4A2,AGPS,KIAA0100,LDLRAD3,PQLC2,ST3GAL2,BICD1,LSM3,TCF7L2,CDC42BPB,ORAI2,AHCYL2,CUX1,LHPP,TXNRD2,RNF149,MUC20,TMEM220,AKR1E2,PSMC1,MCC,MTURN,LSM2,ZBTB12,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,RPRD1A,CFAP43,EFHD2,RFX2,PSMD6,SPIDR,IFI35,MAP3K14,BANK1,SART1,WDR70,MEGF10,ZC3H7B,SLC25A3,PLAGL1,ICAM3,AP1M1,SLC2A5,ITGB3,TMEM51,TRAPPC10,TOP1,AGO2,CNOT10,EXOSC4,LONRF2,MAML3,NR1H3,GZF1,MTA3,NIN,GOLGA3,TINAGL1,HNRNPLL,ARRDC2,ANXA9,WDR8,TMEM241,CLCN1,MED15,PRG3,CARD11,RYR1,HECTD4,RASSF4,MFSD2B,MAK16,GAPVD1,EPB41L2,POLR1C,GSE1,GNAI1,NR3C1,NAA25,SMIM22,HAVCR1,SCOC,ZNF563,TGM3,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,NOV,CRISPLD2,CCDC50,IQSEC1,CYP3A43,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,GALNS,SLC39A7,TOR2A,EPHX4,NT5E,UST,ZRANB1,OSBPL6,TRIM71,SLC39A3,SRPK1,BEND6,RBM14,AGER,NANS,MIR101-2,PLB1,ETV6,YEATS2,VPS52,E2F7,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,PTDSS1,FBXW11,OLFML2A,MIEF2,LOXL1,OGDH,ZZEF1,CTDSPL,PAM16,MAN1A1,RAB40C,NUP93,ADGRV1,TRIM26,SLC22A23,SPPL3,EYA3,PROCA1,SDCCAG8,PLA2G6,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,REV1,PEBP4,DYRK2,RXRB,HNF1B,PLEKHA6,DDX27,APOL3,LDB2,SPATA24,DMXL1,ATXN7L1,GALNTL6,STAT4,TRAF1,F5,MAPK1,ST6GALNAC4,KLHL29,USP39,TTC23,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,SFMBT1,PIGV,BAZ1A,TMEM123,SUSD1,PHF1,HSD17B12,SIRPG,PMM1,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,RANBP3,SPATA5,ARAP1,POLR1A,TUBD1,N4BP2L2,RNF103-CHMP3,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,ABHD12,NOTCH2,SEPHS1,CYB5R3,SMURF2,DTD1,ADGRG6,EPHX1,SHMT2,VANGL1,ADRBK2,OR52B6,CCL23,ARID4A,CRYBB1,PELI1,LIMD1,CHST15,HCN3,SPIRE1,RAB7A,TCF7,FMNL1,SPTBN2,SCN4A,ARHGAP10,HLCS,ECT2L,PEX2,FARP2,STX2,KLHDC7A,L3MBTL1,IDO1,KRT2,NAA16,EPS8L3,BHLHE40,GPD1,TXNDC11,PIWIL2,CELF2,SETMAR,FYN,RBKS,UPF1,ADAP1,POLR3A,SIAE,THEMIS2,ABTB2,MED13L,ANKRD11,SPOP,LRIT3,TSNAX-DISC1,HADH,FAM83A,PPP3R1,STK10,LSG1,KIF6,GID8,MSH4,ZC3H7A,RNF13,EPAS1,CPM,PER2,ASAP2,WWC2,ERMN,PROK1,ARL6IP6,TRPM3,TMEM63A,TRIM29,EIF1AD,PCGF3,PIK3CB,GNS,SPECC1,NAT9,PPP2R5B,RAB19,CLMN,STAT3,SLAMF1,SYN3,MEF2C,MAP4K5,EEFSEC,PYCR1,BUD13,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,GRK4,TMEM17,TIGD1,CXCR4,TMEM201,OR2B2,DAZAP1,PGM1,IMMT,SIGLEC10,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,PEX11G,CACNB2,COL4A3BP,IDNK,TAF6,NPPA,MAP4,DNAH3,ARHGAP12,RMDN3,EFCAB5,ARFGEF2,MAP3K8,VEGFA,EME1,LRCH1,UQCRH,CPA1,ADAM12,MN1,LCLAT1,PLEKHM3,FTL,PRDM16,FAR2,CPEB3,CDK14,TMEM203,FAM102A,APP,GPSM1,SEC62,PRIM2,THAP4,YARS,SUSD4,RASSF1,CSAD,SLC35C1,IGF2BP2,SENP7,CRB1,AUTS2,CHSY1,XPO6,RUNX3,PDXDC1,ZNF852,CLK2,ACOXL,ZFYVE21,LAPTM4A,HBZ,FADS1,RALGPS1,SRP68,DBNL,ADORA1,PLA2G4F,MAST2,PHF21A,CRTAM,GDA,ZBTB16,SYK,C1orf174,MAPKAP1,ADIPOR2,TIMP2,RFFL,DPEP2,H6PD,AFF3,RIOK2,OR6B1,NTRK1,CDK2,CYSTM1,CHPT1,C22orf15,RPS6KA4,ECHDC1,GPR107,ANXA2,PPARA,GTPBP2,EIF3M,GNB1,KRT71,FGF1,JMJD1C,AGL,ELOVL6,SIK2,DHRS9,JSRP1,SNX10,SHCBP1L,SGK2,ANTXR2,YWHAE,SLFN14,PHACTR2,KAZN,WDR1,SLA,AKT3,JAZF1,SEMA4A,SDC1,DNAJB13,PTH2R,TLE1,PLA2G15,OLA1,CACFD1,GSAP,MIR3909,SLC12A6,GNAI2,YES1,OR6M1,EXOC6B,TSPAN33,ITGA2B,EREG,AEBP1,TMPRSS9,GPC5,RBM19,CPPED1,SMPD3,CORO7-PAM16,MLLT1,PHACTR3,CPSF6,CREM,GRHL1,SIAH1,ACVR1B,SPAST,ALKBH5,CALD1,PTK2,C15orf48,MBD5,AMBRA1,SLC4A1,HDAC11,ERN1,CCDC12,BASP1,RBPJ,RHOA,ESYT3,ARHGEF3,C2CD3,DOCK4,APBB1IP,TOLLIP,IKBKB,PSMD13,TPPP3,FER,KLF7,FANCA,PDE6B,EBF3,SNUPN,ENPP3,DRC7,CHID1,SETBP1,MRPL10,CAPN10,ZCCHC14,ULK4,STUB1,RDH5,CDK19,CES4A,CYTL1,IGSF3,CAPZA2,PHC3,CCDC167,ENTPD7,KAT5,CEP85,SIPA1L2,CTSA,MAML2,SETD2,PTPRN2,SDK2,TALDO1,CD160,MFSD10,DEDD,FOXO3,CAPN7,FUT4,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,FBXO36,BSCL2,FSCN3,CDCA7,PARN,COL1A1,CLCNKB,ATF7,SEC23B,TRAPPC3,UCKL1,OTOF,FAM118A,TGFBRAP1,DHRS7,IRF2,TIMM22,GSK3B,YWHAZ,SSTR1,SERGEF,SLC38A6,GMEB1,DGCR2,TREM1,EMILIN2,ZC3H4,MAPKAPK2,ORC1,TM7SF3,RHOBTB3,CHD7,TJP3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,C16orf58,RBM34,PAX8,DPP9,CPNE2,SUCNR1,MPV17,PALD1,ASAH2B,ZCCHC24,CLCN6,NME2,CD300LB,VTI1B,MRAP,NPM3,SMCO4,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SARM1,CSRNP2,SHE,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,SIGLEC7,ATP1A1,CTLA4,FAH,TAGAP,PGD,UBXN7,MYB,ANKRD61,CYP4F12,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,PLEKHG6,ECHDC3,KLHL3,ADK,IGF2R,CRTC1,MYT1,UBR1,PHC1,GCNT2,KRT1,LRCH4,NET1,MAPRE2,NEK7,C10orf88,FARP1,PBRM1,STAMBPL1,AMFR,ACSF3,RAB25,CNNM3,RCOR1,RAD51B,CCL26,UBA7,MCF2L,MYO10,LPCAT1,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,HOXA3,RXRA,NOD1,TAOK3,ADGRA3,ACADL,NME7,PARD3B,MYO1H,ZMYND10,EPSTI1,PNRC1,SLFNL1,ZDHHC1,PRKG2,CSNK1G3,FAM110B,TMEM117,KHDRBS3,DAPP1,ZNF438,EDEM2,SCARF2,XPC,GNA13,ABCG8,ALDH1A2,MYOM1,HNF4A,ISM2,KANK1,PLCXD2,WNT3A,TTC28,UBAP1,KRT6B,ZFAND2A,NR6A1,CXXC5,RNF121,SCTR,FNBP1,RBMS1,TAF15,CERK,STX16,DNMT1,TYSND1,MAFF,WEE1,FCRL3,NUGGC,PPCDC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ARHGAP11A,ZFHX3,REPS1,ALDH3B1,PBX1,TSPAN32,ATP8B1,SHROOM3,CCR3,UNC79,KIF21B,VEZF1,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CNGA4,CCDC86,ADCK1,GDPD3,RPL36AL,TTL,CAMTA1,PIGS,NOL10,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,SPATA25,SP110,TP53BP1,ANGPT1,ASPSCR1,C14orf43,PRKCA,RCC1,GLRX5,ABHD8,MDFIC,CCND3,FTO,MARK2,ATP10B,GPR183,CLPB,LCORL,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,BTBD9,UPF3A,FXYD1,RELL1,GET4,SETD5,NFASC,GRK5,TBC1D14,CUX2,RASAL2,COG7,TEX2,NDUFV2,EFNA5,CDH15,ZNF865,AGPAT3,SHB,HPS1,ATP8B2,STX17,SPRED3,CNPY3,XPNPEP3,SORBS2,SLC9C2,PDZRN3,ANKRD10,DCTN2,CXCR6,TPST2,SHPRH,PILRA,BATF,GEMIN5,RDM1,RAPGEF5,MYO1A,SLC39A1,RHBDD1,FAM207A,FCRLB,ADAM9,FDFT1,PARP4,GLE1,METTL9,GSTM4,NSMCE2,KDM4C,NEK6,CREB5,UBE2QL1,BRCA1,DEGS2,TMEM245,ITGB5,MNDA,ZNF507,BTBD11,SERPINB6,TTLL4,HPCAL1,C4orf45,NLRX1,PSMB7,SGK1,METTL8,RAB11FIP3,PPRC1,ACSM6,NRROS,CPSF1,STXBP2,OSBPL8,STAT5B,RRP9,PNPLA2,RNF138,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,ITGA11,SMG9,SP2,RGL1,LIG3,NCAM2,SORL1,TRPM2,RSU1,NFE2,MCF2L2,DCTN5,MFSD12,TAF5L,ITGB7,ALPL,LHFPL2,CTDSPL2,FNTB,TET2,ZKSCAN3,AOAH,CRYM,NDUFA4,ATP6V0A2,CCDC183,PIEZO1,SYCE2,ALPK3,SAMD8,MT2A,SMYD4,CLEC16A,HIBADH,MX1,TRAK2,CKS2,FURIN,UNK,YDJC,WWP1,GTF2F2,MRC2,SLC25A13,UGT1A7,SNTB1,SLC38A11,RAB7L1,FRYL,DRAP1,ARPC4,LTB4R,SLC13A4,SLC16A3,KRT31,RPA1,RBM44,TEC,FANCC,HCRTR1,SMAD5,ANXA4,SIRPA,TOX,KMT2D,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,KLRD1,BAHCC1,PEX11A,INPP1,ECM2,ACSL6,STARD10,POPDC2,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,SPOCK1,UBE2K,SCAND1,EVI5L,TGFBR2,TULP4,CD82,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,PPM1L,ZNF215,GNA14,NUSAP1,GJA4,ZFC3H1,EHD4,PTPRF,LMO4,LEPROTL1,ITPR2,SLC38A1,EXOC4,TG,MYEOV,FEM1C,RNF145,DCUN1D1,ZBTB7A,USP46,DHRS4,MYO5A,FBN1,RET,DUS2,TCF4,RNF11,ZNF827,CHCHD6,ZNF710,DNAJA3,ARHGEF4,MDM1,CCAR1,REXO2,FAM81B,ARHGAP35,ANP32B,LRP1B,ANKRD44,EDRF1,BCL7B,TMEM130,ASL,SHANK2,NFIL3,THRSP,EEPD1,DLK1,ZBTB20,ATAD5,MKNK1,IRF7,MAT2B,HSPG2,C11orf48,PRIMPOL,BNIP3L,KCNK6,ATP6V1H,ARID2,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,IL18R1,KIF13B,KCNK10,SLC16A10,STK24,ENPP2,BET1L,CCDC74B,ANKRD6,GPR132,FLT3,WDR37,PM20D2,LRP4,ZNF638,SLC30A1,ALKBH2,RRBP1,GLUL,TTC22,ANKS6,PIGR,MATN1,AKIRIN1,HRH2,PDE7A,ETV3,TRAPPC12,SLC27A3,DHX8,SLC8B1,APOLD1,NRXN3,PIEZO2,VRK1,PARP16,KCNE2,EDARADD,RSPRY1,ART4,NLK,FSTL4,PRKCQ,SLC38A10,C11orf68,TGM7,KDM6B,TNFAIP1,RCSD1,CERKL,PPIC,TLL2,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,PLD4,LUZP6,HIF1AN,BAG2,KIF5B,LMO2,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,ITGB6,LGR4,CSF3R,CABLES1,SCAF8,DCLK3,PRPF38B,IL18RAP,BUD31,UTRN,RFC4,ATP2A2,STK11IP,FRY,MDN1,AKT2,ARMC4,PRDX3,MAP4K1,KLRK1,ANKH,MPL,DCP2,SIN3B,HRK,C6orf89,TBL1XR1,OSGIN1,PARP10,ZNF131,MCFD2,URGCP,CCDC141,NEIL2,FGF18,CD58,CRIM1,SNRNP70,TRIM2,ZNF552,RTP2,TRAM2,FNIP1,TP53BP2,ADAMTS7,LAPTM4B,FAM91A1,MOB1A,PIAS1,CLYBL,IVNS1ABP,KNDC1,JDP2,RALGPS2,ARSK,NRXN2,ZSCAN12,SRSF7,RAB3IL1,ZBTB17,SGPP1,PARP1,NCAPD2,TTBK2,ZBTB38,SLC4A8,CYBRD1,NTAN1,FARS2,MEGF11,MFF,LRRC42,SPPL2B,ITGB4,TRPM7,CDH18,TMEM79,SLC37A1,ARMC9,PRDM2,WFDC5,CAT,OSBPL10,FBXW7,MERTK,LILRA1,HNF1A,PSMD1,SCG3,CDC25C,RAD52,MTSS1,ADAM11,PLXNC1,NR1I2,LRFN1,RUNX1,UBASH3A,SNX4,TACR2,ZSCAN25,CRLF3,ZC3H12C,SGIP1,STAT6,SNX30,FNBP4,CTDSP2,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,HPSE2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SPSB4,SEL1L3,HS6ST1,NECAB1,EZR,AHI1,CPB1,CTSS,GABRR2,STARD3,DUT,GNPNAT1,CCDC96,SPATA16,RNF130,ARHGEF10L,LRRFIP2,FKBP11,ZNF333,PLA2G4A,HYAL2,CA12,ATG16L1,OR10P1,CMTM7,ICA1,MTA1,PADI6,CLTC,IFFO1,CKLF,KIF13A,BBX,TNIP2,RFTN2,MYLIP,SPEF1,SLC25A38,RPGRIP1,MAMDC2,SLC11A2,DENND1B,NDUFB9,HAL,LYN,CENPJ,AKAP2,SERBP1,GAS2L1,ACP6,AKT1,ACR,GRAMD4,UBTD2,TBC1D31,UBXN1,UNC50,KPNA4,SLC1A3,ASXL1,TSPAN31,KCNA10,IL1RAP,ATXN7,PHF2,PEX14,PDE4C,ALPK2,RRS1,MAPK6,DOK4,MOSPD3,TFB1M,GPR39,ST3GAL6,ZADH2,HIPK3,METTL1,LTC4S,CASKIN2,PPTC7,CARD14,ALS2,DTNA,ZNRF2,INPP5D,RAPGEF3,NR2F6,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CUEDC1,CLCC1,A3GALT2,ZGPAT,NCOA2,ACTB,PIGC,TOP2B,ORAI3,CLEC17A,BAIAP2,TNFRSF9,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,PDIK1L,WT1,ST3GAL5,SMPDL3A,ATG10,COPA,ARHGAP9,FBXW4,DNAJC5,CEP83,TSNAXIP1,CSNK1G2,RPS15A,ASB2,CLEC12A,DST,MORF4L1,CLSTN1,PSMG1,ANKRD13B,EPHA10,PCNA,DHRS11,LETM1,LPIN2,UBE2E2,PHB2,TLK1,PDLIM2,BUB3,C1RL,MPPED1,NACC1,LITAF,MYO1F,TMEM19,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,ETV7,SEC24A,PSPN,DIXDC1,TNFRSF10B,MDGA1,SFI1,LIPC,KDM2B,HCLS1,ERN2,MAP2K6,CREB3L1,ODF1,FBXO9,GIPR,IL10RA,LRCH3,DNAJC4,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,ZNF692,ADIPOR1,NDUFS6,RABGAP1L,PKD2,ZNF704,USP1,NARS2,MSRA,C12orf43,ATL1,PAX7,ZMIZ1,GLIS1,DRD2,CD47,EFR3B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,NFIC,UHRF2,C1GALT1,PPP2CB,PEX7,ARAP3,ZNF652,PLAA,IL15,ARNT,NEURL1B,NCR2,SERPINF1,SLC25A10,TMEM45B,CPA3,PGAP2,JPH2,DNAJC13,RAB27A,MRPL55,CREB3L3,BRD7,ATAD3C,MIA3,TRIM62,ZP1,GMPPB,A2ML1,ARID4B,PFKFB4,CEP295,ALOX5,EHMT2,COQ5,ZBTB10,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,CGN,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,CA4,EIF4G3,SMCHD1,OAT,MGST2,DLGAP4,LRP12,FYCO1,C17orf63,MGAM2,MS4A6E,MICU1,SEMA3F,RBFOX2,DCTN4,EAF2,ZNF337,PEAK1,FLOT1,CAND2,SPAG4,DNASE1,YOD1,NOX3,LMNB1,CXCL3,APLF,LIMCH1,GLYCTK,THSD7A,GNA15,CNKSR3,LOC81691,WIZ,ZDHHC14,ELF1,TSPAN14,STAU2,NFE2L1,OR2AE1,DGAT2,DLC1,ATXN10,ALOX12B,MYRFL,OTULIN,PRR5,YY1AP1,PPP2R1A,CCL28,TMEM50B,DYM,MCCC1,KPNB1,KCNN3,KRI1,CLPTM1,B3GALNT1,NUDT19,GPRC5A,CDH22,ALDH6A1,GALNT11,FAM149B1,CDYL,ACVR2A,RNF224,DBN1,HSPD1,HMOX2,COLGALT2,HIVEP3,TBC1D13,PWWP2A,OIT3,MAP3K4,NAPG,ALCAM,EDEM3,PROK2,CARS,ARMC2,RAB8B,CHST3,RAP1A,TNPO1,MTF1,FGD5,RASGRP3,PSEN1,MRPL16,SGSM2,SMYD5,P2RY6,FER1L6,SOX6,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,TEX14,GRM2,PPP1CA,INTS8,SEC63,FDX1,MPRIP,REEP5,ITFG2,NGLY1,GIT2,USP47,SPIRE2,ZNF516,SPTLC2,KLHL5,GPS2,KLHDC4,RASSF8,ZEB1,WDR7,SEMA6D,MMP28,GMDS,PGS1,C5AR2,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,SBSN,RNF19A,CPT1A,MNT,SEMA4C,GSPT1,QKI,ARL2,BTN3A3,FKBP1B,MRPS14,PWP2,PRSS41,BATF3,IQGAP1,CCDC112,AMPD2,AFTPH,ACIN1,TOR1B,CD6,HBS1L,ANKRD9,NCAM1,ATF6,INPP5E,PDPK1,SLC25A44,MAP2K3,PLCB1,GALNT18,ADD3,CD84,BIK,NUCKS1,ELP6,PRPF8,PACS2,ZNF19,MON2,ALAD,PANK1,CCDC146,EXTL1,RPS6KA1,NEK1,NMNAT1,GTDC1,KIF3B,SUFU,STX1B,CNST,GRK6,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ZZZ3,TGIF2,ESYT2,SLC40A1,GALK2,CACHD1,ZFAND6,RASA2,RB1CC1,SCG5,DFFA,C17orf62,PKNOX1,ST8SIA6,RCBTB2,COG2,IL2RA,RUNX2,NCLN,ST14,PAK2,ALAS1,FLT1,CLCN7,DOCK10,FBL,EMID1,GCNT3,ZNF565,PRKAR2A,ZNF740,RSPH14,PCM1,RNASET2,MTMR7,TRPM5,TNFRSF13C,ZNF518B,OR6P1,ZFAT,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,C1QTNF6,PCOLCE,MARK4,C9orf152,NAGLU,C9orf64,DHX33,SDCBP2,PIK3R3,GLRB,ASB3,JADE2,MAP3K5,MEOX1,ATP6V0D1,ZMYND8,BCAS4,DTHD1,KLHDC3,NPTN,HSPB1,SORBS1,TXNDC2,PIKFYVE,CAMK4,DDA1
## 1561 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,GUSB,TCEA2,MSMP,GNB5,TMED3,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,TET3,FBP1,ELMO1,FBXW8,MITF,SLC25A33,TNIK,TRIM9,PRG2,DAPK2,OSBPL5,TRIO,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,ZNF653,RECQL5,SEC16B,PLD3,MGLL,ANAPC11,MAPK13,NKIRAS2,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,ADARB1,TMEM11,KCNH2,AREL1,EPB41,CAPG,NGFR,SLC2A8,GATAD2A,HMBS,NDST2,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,CHP1,VPS53,ZNF48,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,ERMAP,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,MYRIP,ITGAL,VTI1A,MED25,ZBTB32,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,GNAO1,IRGC,TRIM33,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,SSBP3,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,SLC39A4,TPST1,POR,AXIN1,RD3,ITPR1,CREG1,DEPDC5,CSNK1D,MTCL1,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,NSMCE1,ASH1L,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,PNPLA1,CACNA1S,PI4KB,GYG1,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,CMTM6,CSRP1,GFPT2,DICER1,QRICH2,SERINC5,ITSN1,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,WWP2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,SAFB2,ACSL1,ABR,DOCK1,BCAS1,NEMF,RAB11FIP1,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,RALGDS,NUTF2,TANGO2,ELMO2,COL15A1,GJB3,SGMS1,SPATS2L,POLR2F,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,FOXJ3,CLRN1,HMGCL,KLF16,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,PICALM,GNAQ,MAFK,ADAM8,FZR1,MED27,AQP1,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,PELI2,UPK3A,SIAH2,MICAL2,MYLK,TMOD3,SAP30L,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,ZNF70,IL13,CCNY,DMAP1,ZNF789,SLC23A2,PRX,RREB1,HCFC1R1,ERGIC1,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,SLC12A4,PROZ,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,CATSPER4,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,SEMA3B,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,TOM1L2,NCALD,FECH,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,THYN1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,PPP1R16B,NCK2,ST3GAL4,RNF157,IKZF1,HECW1,MAML1,SLC29A3,SULF2,GSTM3,TGFA,GALNT12,CEBPB,STK3,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,TRIM8,CCSER2,MIB1,C6orf106,HTT,HPD,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,FAM53B,BAIAP2L1,SPTBN1,MYL9,GLB1,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,CD86,SOAT2,FMO1,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,TLDC2,COL20A1,NEDD4L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,RASSF3,ZNF532,SIK3,EML3,SNX9,MCMBP,DNAJC3,KAT8,PLA1A,WNT3,GALNT7,UXS1,MTUS2,DHCR24,EVPL,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,PIGN,CDKN2AIPNL,SERP2,WDFY2,RNF216,TBC1D10A,AGAP3,BACH2,ATG13,NEK8,PHTF2,LARP1,CACNA1D,LRRC8C,P2RX7,SLC11A1,PIK3AP1,P3H2,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,DENND2D,GCM1,RNF41,COL11A2,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,TPM3,CCDC57,CALR3,STON1-GTF2A1L,UBE2G1,PRKDC,DESI1,RFT1,GAS7,MBTPS1,HK1,RIN3,SLC7A11,MLST8,XAF1,DNHD1,ERG,IMPA2,ACRBP,VAMP1,AGXT,NAP1L4,PIGL,NPL,GTPBP1,HPX,CLDN10,VGLL4,GON4L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,NAV2,MAPRE3,LRRC8D,ASB8,ZDHHC18,SMYD3,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,ACAD10,HVCN1,SMG6,RHOBTB2,SND1,MBD6,RCC2,PAFAH2,SLIT3,USP19,ITPRIP,SREBF2,ASIC1,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,THRB,SGSM3,TGFB3,EIF6,GPATCH1,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,WWOX,SEC14L2,NAPA,LEF1,OSBP2,RIBC2,HDC,PRNP,RHBDD2,C16orf70,IQCD,DHX30,PRDM10,THG1L,KRT72,ZNF609,CREB3L2,NIPSNAP3B,ATP2A3,AHNAK,MIDN,VEGFB,DNAH1,B3GALNT2,HNMT,THADA,MDM4,ELL2,ZDHHC7,RAPGEF1,CTSK,AGBL4,PDZD8,IL16,HDAC4,EXT1,ACTN4,EPN2,ARPP19,GPD2,C16orf45,FCGR2A,ENO3,XPR1,ZNF699,RBPMS,ARSG,RASGRP1,ITGA2,OPA3,HNRNPM,SIPA1L3,RMND1,ARL6IP4,CTSZ,PTPN18,LGR5,INPP5F,IL1B,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,SRGAP3,PTPN1,B4GALT7,AAK1,BEST1,LIMK1,CDK5RAP3,FBXL2,RAB3B,EHMT1,ZXDC,ABAT,ANO6,IKZF2,STOML1,POMGNT1,TSPAN2,PIK3R5,FBF1,TMOD1,MAP2K5,UBE2D3,PHF12,ALDH2,TOP1MT,RALY,DIDO1,ZNF175,LCP1,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,ATP2C1,RNF43,EHBP1,HPS4,CHCHD3,ZNFX1,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,EMC1,FOXN3,TAOK2,MCPH1,POC1A,LAX1,KLF13,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ERP29,ADAM19,PCCA,TBL2,STT3A,CDX1,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,CHST11,P4HTM,DGKG,MBOAT1,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,MTA2,PADI2,KCNIP2,RASGRF2,SIL1,LSM14A,INSC,LFNG,LGALS12,GDPD5,MYO9B,DNAJC18,SUPT3H,PPP2R5C,OPALIN,SLC35D1,RNF24,CD4,DNAH2,CEACAM1,TLE4,TTC17,USPL1,DNMT3A,MACF1,SRF,ZBTB34,TMED10,LGR6,PDE9A,AACS,P4HB,MICAL1,ACAD8,MRPS27,TUBGCP2,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,MTFR1,ERAP2,ODC1,RAB20,YWHAQ,CSDE1,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,IL1RN,PLEKHA7,SLC39A2,ZBTB42,DNAJC6,ACO1,WDR46,GABARAPL1,MAPKAPK3,CHD9,SLC7A14,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SF3A1,SARNP,TESK2,ATG7,ACSF2,SCAF11,RHOH,SRC,PCBP2,SACS,C20orf203,MTHFD2,TBXAS1,CRTC3,PDE4D,SPI1,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,CCBL1,DDX56,DHX15,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,ARHGAP24,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,EPC1,PPP2R5E,RFC3,TRIM16,MARK3,NACC2,CAMP,BBS1,RASSF5,ATXN1,ARID5B,CLTCL1,HDAC9,TMCC2,ARFGAP2,EPHA4,GLIPR2,MCU,MLXIP,NBPF20,SLC25A45,MBNL2,MCCC2,KCNA2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,SIN3A,STIM2,KIF26A,UPP2,ARHGEF7,SYTL3,BCL9,CHMP1A,FAIM2,VDR,RAD21,CEBPE,SPECC1L-ADORA2A,CFAP45,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,DEPDC1B,SKI,KCNE1,PPM1A,HIF1A,SAG,DOCK2,ILKAP,TNRC18,HIVEP2,EIF4EBP1,RGS9,EEF2K,TRPM4,NCOA7,ASH2L,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,PDE4DIP,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,SNCAIP,HMGXB4,SLMAP,PTP4A2,CCDC136,AGPS,PQLC2,ST3GAL2,BICD1,LSM3,TCF7L2,CDC42BPB,AHCYL2,CUX1,LHPP,TXNRD2,RNF149,MUC20,TXNDC8,AKR1E2,PSMC1,MCC,MTURN,LSM2,ZBTB12,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,RPRD1A,CFAP43,RFX2,PSMD6,SPIDR,IFI35,MAP3K14,SART1,WDR70,ZC3H7B,SLC25A3,PLAGL1,AP1M1,SLC2A5,ITGB3,TRAPPC10,TOP1,AGO2,CNOT10,EXOSC4,MAML3,NR1H3,GZF1,MTA3,NIN,GOLGA3,TINAGL1,HNRNPLL,ARRDC2,ANXA9,WDR8,TMEM241,MED15,PRG3,CARD11,RYR1,MAK16,GAPVD1,EPB41L2,GAPT,POLR1C,GNAI1,NR3C1,NAA25,SMIM22,SCOC,ZNF563,TGM3,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,NOV,CRISPLD2,CCDC50,IQSEC1,CYP3A43,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,GALNS,SLC39A7,TOR2A,NT5E,UST,ZRANB1,OSBPL6,TRIM71,EFR3A,SRPK1,BEND6,RBM14,AGER,NANS,ETV6,YEATS2,VPS52,E2F7,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,PTDSS1,FBXW11,MIEF2,LOXL1,OGDH,CTDSPL,PAM16,MAN1A1,RAB40C,NUP93,ADGRV1,TRIM26,SPPL3,EYA3,SDCCAG8,PLA2G6,BDKRB2,SNAP47,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,REV1,PEBP4,DYRK2,RXRB,HNF1B,APOL3,LDB2,SPATA24,DMXL1,GALNTL6,STAT4,TRAF1,F5,MAPK1,ST6GALNAC4,USP39,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,SFMBT1,PIGV,BAZ1A,TMEM123,PHF1,HSD17B12,PMM1,ZNF628,PTPRC,AP2B1,ZC3H14,RANBP3,SPATA5,ARAP1,POLR1A,TUBD1,N4BP2L2,RNF103-CHMP3,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,ABHD12,NOTCH2,SEPHS1,CYB5R3,SMURF2,DTD1,ADGRG6,EPHX1,SHMT2,ADRBK2,ARID4A,PELI1,LIMD1,CHST15,SPIRE1,RAB7A,TCF7,FMNL1,SPTBN2,ARHGAP10,HLCS,PEX2,FARP2,STX2,L3MBTL1,IDO1,KRT2,NAA16,EPS8L3,BHLHE40,GPD1,TXNDC11,PIWIL2,CELF2,SETMAR,FYN,RBKS,UPF1,ADAP1,POLR3A,SIAE,THEMIS2,MED13L,ANKRD11,SPOP,LRIT3,HADH,FAM83A,PPP3R1,STK10,LSG1,KIF6,GID8,MSH4,ZC3H7A,RNF13,EPAS1,PER2,ASAP2,WWC2,ERMN,ARL6IP6,TMEM63A,TRIM29,EIF1AD,PCGF3,PIK3CB,GNS,SPECC1,PPP2R5B,CLMN,STAT3,SLAMF1,SYN3,MEF2C,MAP4K5,EEFSEC,PYCR1,BUD13,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,GRK4,TIGD1,CXCR4,TMEM201,FAM53A,DAZAP1,PGM1,IMMT,CEP128,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,PEX11G,COL4A3BP,TAF6,NPPA,MAP4,DNAH3,ARHGAP12,RMDN3,ARFGEF2,MAP3K8,VEGFA,EME1,LRCH1,UQCRH,ADAM12,MN1,LCLAT1,PLEKHM3,FTL,PRDM16,FAR2,CPEB3,CDK14,TMEM203,APP,GPSM1,SEC62,PRIM2,YARS,RASSF1,CSAD,SLC35C1,IGF2BP2,SENP7,AUTS2,CHSY1,XPO6,RUNX3,PDXDC1,ZNF852,CLK2,ACOXL,ZFYVE21,LAPTM4A,HBZ,FADS1,RALGPS1,SRP68,DBNL,ADORA1,PLA2G4F,MAST2,PHF21A,GDA,ZBTB16,SYK,C1orf174,MAPKAP1,TIMP2,RFFL,H6PD,AFF3,RIOK2,NTRK1,CDK2,CYSTM1,CHPT1,RPS6KA4,ECHDC1,GPR107,ANXA2,PPARA,GTPBP2,EIF3M,GNB1,KRT71,FGF1,JMJD1C,AGL,ELOVL6,SIK2,DHRS9,JSRP1,SNX10,SHCBP1L,SGK2,ANTXR2,YWHAE,GGNBP2,SLFN14,PHACTR2,KAZN,WDR1,SLA,AKT3,JAZF1,SDC1,DNAJB13,TLE1,PLA2G15,OLA1,GSAP,GNAI2,YES1,EXOC6B,TSPAN33,ITGA2B,EREG,AEBP1,GPC5,RBM19,CPPED1,SMPD3,CORO7-PAM16,MLLT1,PHACTR3,CPSF6,CREM,GRHL1,SIAH1,ACVR1B,SPAST,ALKBH5,CALD1,PTK2,C15orf48,MBD5,AMBRA1,SLC4A1,HDAC11,ERN1,CCDC12,BASP1,RBPJ,RHOA,ESYT3,ARHGEF3,C2CD3,DOCK4,APBB1IP,TOLLIP,IKBKB,PSMD13,TPPP3,FER,KLF7,FANCA,EBF3,SNUPN,ENPP3,DRC7,CHID1,SETBP1,MRPL10,CAPN10,STUB1,RDH5,CDK19,CAPZA2,PHC3,ENTPD7,KAT5,CEP85,SIPA1L2,CTSA,MAML2,SETD2,PTPRN2,TALDO1,MFSD10,DEDD,FOXO3,CAPN7,FUT4,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,BSCL2,FSCN3,CDCA7,PARN,COL1A1,ATF7,SEC23B,TRAPPC3,NUP210,UCKL1,OTOF,TGFBRAP1,IRF2,TIMM22,GSK3B,YWHAZ,SSTR1,SERGEF,GMEB1,ZC3H4,MAPKAPK2,ORC1,RHOBTB3,CHD7,TJP3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,RBM34,PAX8,DPP9,CPNE2,MPV17,PALD1,CLCN6,NME2,VTI1B,MRAP,NPM3,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SLC7A6OS,SARM1,CSRNP2,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,ATP1A1,CTLA4,FAH,TAGAP,PGD,UBXN7,MYB,ANKRD61,CYP4F12,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,PLEKHG6,ECHDC3,KLHL3,ADK,IGF2R,CRTC1,MYT1,UBR1,PHC1,GCNT2,KRT1,LRCH4,NET1,MAPRE2,NEK7,C10orf88,FARP1,PBRM1,STAMBPL1,AMFR,ACSF3,RAB25,CNNM3,RCOR1,RAD51B,UBA7,MCF2L,MYO10,LPCAT1,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,HOXA3,RXRA,NOD1,TAOK3,ACADL,NME7,PARD3B,MYO1H,ZMYND10,PNRC1,ZDHHC1,PRKG2,CSNK1G3,FAM110B,TMEM117,KHDRBS3,DAPP1,ZNF438,EDEM2,XPC,GNA13,ALDH1A2,MYOM1,HNF4A,KANK1,PLCXD2,WNT3A,TTC28,UBAP1,KRT6B,ZFAND2A,NR6A1,CXXC5,RNF121,SCTR,FNBP1,RBMS1,TAF15,CERK,STX16,DNMT1,TYSND1,MAFF,WEE1,NUGGC,PPCDC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ARHGAP11A,ZFHX3,REPS1,ALDH3B1,PBX1,ATP8B1,SHROOM3,CCR3,KIF21B,VEZF1,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CNGA4,CCDC86,ADCK1,GDPD3,RPL36AL,TTL,CAMTA1,PIGS,NOL10,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,SP110,TP53BP1,ASPSCR1,C14orf43,PRKCA,RCC1,GLRX5,ABHD8,MDFIC,CCND3,FTO,MARK2,ATP10B,CLPB,LCORL,FAM168B,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,UPF3A,RELL1,GET4,SETD5,NFASC,GRK5,TBC1D14,CUX2,RASAL2,COG7,TEX2,NDUFV2,CDH15,ZNF865,AGPAT3,SHB,HPS1,ATP8B2,STX17,CNPY3,XPNPEP3,SORBS2,PDZRN3,DCTN2,TPST2,SHPRH,BATF,GEMIN5,RDM1,RAPGEF5,MYO1A,SLC39A1,RHBDD1,FAM207A,FCRLB,FDFT1,PARP4,GLE1,GSTM4,NSMCE2,KDM4C,NEK6,CREB5,UBE2QL1,BRCA1,DEGS2,ITGB5,MNDA,ZNF507,SERPINB6,TTLL4,NLRX1,PSMB7,SGK1,METTL8,RAB11FIP3,PPRC1,ACSM6,NRROS,CPSF1,STXBP2,OSBPL8,STAT5B,RRP9,PNPLA2,RNF138,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,SMG9,SP2,RGL1,LIG3,NCAM2,SORL1,TRPM2,RSU1,NFE2,DCTN5,MFSD12,TAF5L,LHFPL2,CTDSPL2,FNTB,TET2,ZKSCAN3,AOAH,CRYM,NDUFA4,ATP6V0A2,PIEZO1,SYCE2,ALPK3,SAMD8,MT2A,CLEC16A,HIBADH,MX1,TRAK2,FURIN,UNK,WWP1,GTF2F2,SLC25A13,UGT1A7,SNTB1,RAB7L1,FRYL,DRAP1,ARPC4,SLC16A3,KRT31,RPA1,RBM44,TEC,FANCC,SMAD5,ANXA4,SIRPA,TOX,KMT2D,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,PEX11A,INPP1,ACSL6,STARD10,MYCT1,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,SPOCK1,UBE2K,SCAND1,TGFBR2,TULP4,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,PPM1L,ZNF215,GNA14,NUSAP1,ZFC3H1,LYRM1,EHD4,LMO4,LEPROTL1,ITPR2,EXOC4,FEM1C,RNF145,DCUN1D1,ZBTB7A,USP46,DHRS4,MYO5A,FAM174B,FBN1,RET,DUS2,TCF4,RNF11,ZNF827,CHCHD6,ZNF710,DNAJA3,ARHGEF4,MDM1,CCAR1,REXO2,FAM81B,ARHGAP35,ANP32B,EDRF1,TMEM130,ASL,SHANK2,NFIL3,THRSP,DLK1,ZBTB20,ATAD5,MKNK1,IRF7,MAT2B,HSPG2,C11orf48,PRIMPOL,BNIP3L,ATP6V1H,ARID2,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,KIF13B,SLC16A10,STK24,BET1L,ANKRD6,FLT3,WDR37,PM20D2,ZNF638,SLC30A1,ALKBH2,RRBP1,GLUL,ANKS6,PIGR,AKIRIN1,PDE7A,ETV3,TRAPPC12,SLC27A3,DHX8,SLC8B1,VRK1,PARP16,KCNE2,EDARADD,RSPRY1,NLK,FSTL4,PRKCQ,SLC38A10,KDM6B,TNFAIP1,RCSD1,CERKL,PPIC,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,PLD4,LUZP6,HIF1AN,BAG2,KIF5B,LMO2,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,ITGB6,CABLES1,SCAF8,DCLK3,PRPF38B,BUD31,UTRN,CSRP2BP,RFC4,ATP2A2,STK11IP,FRY,MDN1,AKT2,ARMC4,PRDX3,MPL,DCP2,SIN3B,HRK,C6orf89,TBL1XR1,PARP10,ZNF131,MCFD2,URGCP,CCDC141,NEIL2,FGF18,CD58,SNRNP70,TRIM2,ZNF552,TRAM2,FNIP1,TP53BP2,ADAMTS7,LAPTM4B,FAM91A1,MOB1A,PIAS1,CLYBL,IVNS1ABP,JDP2,RALGPS2,ARSK,ZSCAN12,SRSF7,RAB3IL1,ZBTB17,SGPP1,PARP1,NCAPD2,TTBK2,ZBTB38,SLC4A8,ACTRT2,CYBRD1,NTAN1,FARS2,MFF,SPPL2B,ITGB4,FRMD4B,TMEM79,SLC37A1,ARMC9,PRDM2,CAT,OSBPL10,FBXW7,MERTK,HNF1A,PSMD1,SCG3,CDC25C,RAD52,MTSS1,NR1I2,RUNX1,UBASH3A,SNX4,ZSCAN25,CRLF3,ZC3H12C,SGIP1,STAT6,FNBP4,CTDSP2,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SPSB4,SEL1L3,HS6ST1,NECAB1,EZR,AHI1,TMEM64,CTSS,STARD3,DUT,GNPNAT1,CCDC96,SPATA16,RNF130,ARHGEF10L,ZNF333,AAR2,PLA2G4A,HYAL2,ATG16L1,ICA1,MTA1,PADI6,CLTC,IFFO1,KIF13A,BBX,TNIP2,MYLIP,SPEF1,SLC25A38,RPGRIP1,MAMDC2,SLC11A2,DENND1B,NDUFB9,HAL,LYN,CENPJ,SERBP1,GAS2L1,ACP6,VWA3B,AKT1,ACR,GRAMD4,UBTD2,TBC1D31,UBXN1,UNC50,KPNA4,SLC1A3,ASXL1,ATXN7,PHF2,PEX14,PDE4C,RRS1,MAPK6,DOK4,MOSPD3,TFB1M,ST3GAL6,ZADH2,HIPK3,METTL1,LTC4S,CASKIN2,GULP1,PPTC7,CARD14,ALS2,DTNA,ZNRF2,INPP5D,RAPGEF3,NR2F6,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CLCC1,A3GALT2,ZGPAT,NCOA2,ACTB,PIGC,TOP2B,MEIKIN,BAIAP2,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,PDIK1L,WT1,ST3GAL5,ATG10,COPA,ARHGAP9,FBXW4,DNAJC5,CEP83,TSNAXIP1,CSNK1G2,RPS15A,ASB2,CLEC12A,DST,MORF4L1,CLSTN1,PSMG1,ANKRD13B,PCNA,LETM1,LPIN2,UBE2E2,PHB2,TLK1,PDLIM2,BUB3,NACC1,LITAF,MYO1F,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,ETV7,SEC24A,DIXDC1,MDGA1,SFI1,LIPC,KDM2B,HCLS1,ERN2,MAP2K6,CREB3L1,ODF1,FBXO9,IL10RA,LRCH3,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,ZNF692,NDUFS6,RABGAP1L,PKD2,ZNF704,USP1,NARS2,MSRA,C12orf43,ATL1,PAX7,ZMIZ1,GLIS1,DRD2,CD47,EFR3B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,NFIC,UHRF2,C1GALT1,PPP2CB,PEX7,ARAP3,ZNF652,PLAA,IL15,ARNT,NEURL1B,SERPINF1,SLC25A10,TMEM168,CPA3,PGAP2,JPH2,DNAJC13,RAB27A,MRPL55,CREB3L3,BRD7,ATAD3C,MIA3,TRIM62,GMPPB,ARID4B,PFKFB4,CEP295,ALOX5,EHMT2,COQ5,ZBTB10,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,CGN,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,CA4,EIF4G3,SMCHD1,OAT,MGST2,FYCO1,C17orf63,MICU1,RBFOX2,DCTN4,EAF2,ZNF337,PEAK1,FLOT1,CAND2,SPAG4,DNASE1,YOD1,NOX3,LMNB1,APLF,LIMCH1,GLYCTK,GNA15,CNKSR3,LOC81691,WIZ,ZDHHC14,ELF1,TSPAN14,STAU2,NFE2L1,DGAT2,DLC1,ATXN10,ALOX12B,MYRFL,OTULIN,PRR5,YY1AP1,PPP2R1A,TMEM50B,DYM,MCCC1,KPNB1,KCNN3,KRI1,B3GALNT1,NUDT19,GPRC5A,ALDH6A1,GALNT11,CDYL,ACVR2A,DBN1,HSPD1,HMOX2,COLGALT2,HIVEP3,TBC1D13,PWWP2A,OIT3,MAP3K4,NAPG,EDEM3,CARS,RAB8B,CHST3,RAP1A,TNPO1,MTF1,FGD5,RASGRP3,PSEN1,MRPL16,SGSM2,SOX6,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,TEX14,PPP1CA,INTS8,SEC63,FDX1,MPRIP,REEP5,ITFG2,NGLY1,GIT2,USP47,SPIRE2,ZNF516,SPTLC2,KLHL5,GPS2,ZEB1,WDR7,SEMA6D,MMP28,GMDS,PGS1,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,RNF19A,CPT1A,MNT,SEMA4C,GSPT1,QKI,ARL2,ALG14,FKBP1B,MRPS14,PWP2,BATF3,IQGAP1,AMPD2,AFTPH,ACIN1,TOR1B,HBS1L,ANKRD9,NCAM1,ATF6,INPP5E,PDPK1,SLC25A44,MAP2K3,PLCB1,GALNT18,ADD3,CD84,BIK,NUCKS1,ELP6,PRPF8,PACS2,ZNF19,MON2,ALAD,PANK1,CCDC146,EXTL1,RPS6KA1,NEK1,NMNAT1,KIF3B,SUFU,STX1B,CNST,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ZZZ3,TGIF2,ESYT2,SLC40A1,GALK2,ZFAND6,RASA2,RB1CC1,SCG5,DFFA,C17orf62,PKNOX1,ST8SIA6,RCBTB2,COG2,RUNX2,NCLN,PAK2,ALAS1,FLT1,CLCN7,DOCK10,FBL,EMID1,GCNT3,ZNF565,C1orf9,PRKAR2A,ZNF740,PCM1,RNASET2,MTMR7,ZNF518B,ZFAT,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,MARK4,NAGLU,DHX33,SDCBP2,PIK3R3,GLRB,ASB3,JADE2,MAP3K5,MEOX1,ATP6V0D1,ZMYND8,BCAS4,KLHDC3,HSPB1,SORBS1,TXNDC2,PIKFYVE,CAMK4,DDA1
## 1562 ACOT7,SEC31B,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,PTAFR,GUSB,MSMP,GNB5,TMED3,EVL,AKAP1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,TET3,FBP1,ELMO1,FBXW8,MITF,SLC25A33,TNIK,TRIM9,PRG2,DAPK2,OSBPL5,TRIO,XXYLT1,TRIM4,UBE2O,ARID3A,SLC25A26,RECQL5,SEC16B,PLD3,MGLL,ANAPC11,MAPK13,NKIRAS2,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,ACOX1,ATG14,NENF,SMURF1,RNF220,VKORC1L1,DDC,MFHAS1,PTPRS,ADARB1,TMEM11,KCNH2,AREL1,EPB41,CAPG,NGFR,SLC2A8,HMBS,NDST2,PCSK6,NOLC1,MINK1,CLC,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,UQCC1,HORMAD2,MAP3K7CL,CCM2,EPHB2,CHP1,VPS53,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,ERMAP,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,MYRIP,ITGAL,VTI1A,SYNDIG1,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,HHAT,GALNT6,TBC1D5,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,HEXA,MTMR3,TFR2,SH3GL1,GGCX,NDOR1,PDCL,BCKDHA,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,SLC39A4,TPST1,POR,AXIN1,RD3,ITPR1,CREG1,DEPDC5,CSNK1D,MTCL1,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,SERPINC1,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,RNF122,PRKCB,GALNT16,MAP3K1,PNPLA1,CACNA1S,PI4KB,GYG1,HK2,DYRK1A,MLX,DAG1,KRT8,LGALS8,WIPI1,URI1,UBXN11,AMPD3,SWAP70,CEL,TVP23B,BIN3,CMTM6,CSRP1,GFPT2,DICER1,QRICH2,SERINC5,ITSN1,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,WWP2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,SAFB2,ACSL1,ABR,DOCK1,BCAS1,RAB11FIP1,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,RALGDS,NUTF2,TANGO2,ELMO2,COL15A1,GJB3,SGMS1,SPATS2L,POLR2F,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,CLRN1,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,PDLIM7,APTX,SLC17A4,CS,UBAC2,NAPB,PTPRJ,CORO1C,MFSD2A,ASAP1,PICALM,GNAQ,ADAM8,FZR1,MED27,AQP1,DENND3,FCHSD2,CDH1,OAZ2,PSTPIP2,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,PELI2,UPK3A,SIAH2,MYLK,TMOD3,SMARCC1,RALA,PRKCE,GPI,ARHGAP26,PAK6,IL13,CCNY,DMAP1,SLC23A2,PRX,RREB1,HCFC1R1,ERGIC1,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,SLC12A4,PROZ,USP20,TAF4B,RPS6KA2,LRSAM1,CATSPER4,RNF40,AK8,RBL2,GSN,HCK,TRAF3,SEMA3B,TPCN1,MCM2,CAB39,GALM,MAP6,PPP1R1B,TOM1L2,NCALD,FECH,RNF10,FOXK1,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,DTNB,PPP1R16B,NCK2,ST3GAL4,RNF157,IKZF1,HECW1,SLC29A3,SULF2,GSTM3,TGFA,GALNT12,CEBPB,STK3,ARID1B,KPNA1,CAPZB,GNG7,TRIM8,CCSER2,MIB1,C6orf106,HTT,HPD,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,BAIAP2L1,SPTBN1,MYL9,GLB1,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,SOAT2,FMO1,MAN1C1,POLR3E,METTL16,RAP1GAP2,COL20A1,NEDD4L,RASSF2,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,RASSF3,SIK3,EML3,SNX9,MCMBP,DNAJC3,PLA1A,WNT3,GALNT7,UXS1,MTUS2,DHCR24,EVPL,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,CD151,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,ABHD2,TESPA1,GRAP2,TOPBP1,PACSIN2,UBR4,PIGN,SERP2,WDFY2,RNF216,TBC1D10A,AGAP3,BACH2,ATG13,NEK8,PHTF2,LARP1,CACNA1D,LRRC8C,P2RX7,SLC11A1,PIK3AP1,P3H2,OSBPL3,SEPT9,CAPN2,DENND2D,RNF41,COL11A2,NMT2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,USP12,UCP3,NPRL3,TPM3,CCDC57,CALR3,STON1-GTF2A1L,UBE2G1,PRKDC,DESI1,RFT1,GAS7,MBTPS1,HK1,RIN3,SLC7A11,MLST8,XAF1,DNHD1,ERG,IMPA2,ACRBP,VAMP1,AGXT,NAP1L4,PIGL,NPL,GTPBP1,HPX,CLDN10,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,MAPRE3,LRRC8D,ASB8,ZDHHC18,SMYD3,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,ACAD10,HVCN1,SMG6,RHOBTB2,SND1,RCC2,PAFAH2,SLIT3,USP19,SREBF2,ASIC1,RAB31,LMAN2L,MYBPC3,SMAD7,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,RALBP1,RIC8B,PHACTR1,COL4A1,WWOX,SEC14L2,NAPA,LEF1,OSBP2,HDC,PRNP,RHBDD2,C16orf70,IQCD,DHX30,THG1L,KRT72,CREB3L2,NIPSNAP3B,ATP2A3,AHNAK,MIDN,VEGFB,DNAH1,B3GALNT2,HNMT,THADA,ZDHHC7,RAPGEF1,CTSK,AGBL4,PDZD8,IL16,HDAC4,EXT1,ACTN4,EPN2,ARPP19,GPD2,FCGR2A,ENO3,XPR1,RBPMS,ARSG,RASGRP1,ITGA2,OPA3,HNRNPM,SIPA1L3,RMND1,CTSZ,PTPN18,LGR5,INPP5F,IL1B,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,TOP3A,SRGAP3,PTPN1,B4GALT7,AAK1,BEST1,LIMK1,CDK5RAP3,FBXL2,RAB3B,ABAT,ANO6,STOML1,POMGNT1,PIK3R5,FBF1,TMOD1,MAP2K5,UBE2D3,ALDH2,TOP1MT,DIDO1,ZNF175,LCP1,PARP9,CLSTN3,PHKB,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,ATP2C1,RNF43,EHBP1,HPS4,CHCHD3,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,EMC1,TAOK2,MCPH1,POC1A,LAX1,MGAT4B,CTNS,GPHN,AKAP12,JOSD1,PITPNM2,PRMT3,STX3,PPP3CA,TTLL5,GATB,SECISBP2,ERP29,ADAM19,PCCA,TBL2,STT3A,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,SH2D3C,EIF4G2,CNR2,PELP1,CHST11,P4HTM,DGKG,MBOAT1,PKD2L1,HMGA1,CYFIP2,PXN,CLU,SGPL1,MECOM,PADI2,KCNIP2,RASGRF2,SIL1,LSM14A,INSC,LFNG,LGALS12,GDPD5,MYO9B,DNAJC18,PPP2R5C,OPALIN,SLC35D1,RNF24,CD4,DNAH2,CEACAM1,TTC17,DNMT3A,MACF1,SRF,TMED10,LGR6,PDE9A,AACS,P4HB,MICAL1,ACAD8,MRPS27,TUBGCP2,PAPSS2,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,HIPK2,MTFR1,ERAP2,ODC1,RAB20,YWHAQ,CSDE1,CRABP2,SLC36A1,RSAD2,SLC8A1,TKT,PTEN,PRKAB1,KDELC2,ADD1,IL1RN,PLEKHA7,SLC39A2,ZBTB42,DNAJC6,ACO1,GABARAPL1,MAPKAPK3,CHD9,SLC7A14,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SARNP,TESK2,ATG7,ACSF2,RHOH,SRC,PCBP2,SACS,C20orf203,MTHFD2,TBXAS1,CRTC3,PDE4D,UBE4A,LAIR1,OBSL1,B3GNT8,MVB12B,VPS37B,CCBL1,LRRC59,EXOC3,SMAD4,TFEB,DGAT1,LPP,ARHGAP24,GATA2,ARHGEF18,SMAP2,NDUFV1,DNAJC11,CD28,PPP2R5E,TRIM16,MARK3,NACC2,CAMP,BBS1,RASSF5,ATXN1,CLTCL1,HDAC9,TMCC2,ARFGAP2,EPHA4,GLIPR2,MCU,MLXIP,NBPF20,SLC25A45,MBNL2,MCCC2,KCNA2,CHRM2,CNOT8,KCNQ1,FBXO32,IL1RL1,STIM2,KIF26A,UPP2,ARHGEF7,SYTL3,BCL9,CHMP1A,FAIM2,VDR,RAD21,SPECC1L-ADORA2A,IKZF3,PARK7,PNKD,CAMSAP1,MAEA,ENTHD1,CDK17,FAM20B,DEPDC1B,SKI,KCNE1,PPM1A,HIF1A,SAG,DOCK2,ILKAP,TNRC18,EIF4EBP1,RGS9,EEF2K,TRPM4,SORD,EPS15,RAF1,CMTR1,RAD51C,KDM4A,PDE4DIP,WNT5B,TNFAIP8,CSGALNACT1,ZC3HAV1,SNCAIP,SLMAP,PTP4A2,CCDC136,AGPS,PQLC2,ST3GAL2,BICD1,LSM3,CDC42BPB,AHCYL2,CUX1,LHPP,TXNRD2,RNF149,MUC20,TXNDC8,AKR1E2,PSMC1,MCC,MTURN,LSM2,PAK4,PCNT,KIF1B,WDFY4,USP7,RNF144A,CFAP43,RFX2,PSMD6,IFI35,MAP3K14,SART1,SLC25A3,PLAGL1,AP1M1,SLC2A5,ITGB3,TRAPPC10,TOP1,AGO2,CNOT10,EXOSC4,NR1H3,GZF1,MTA3,NIN,GOLGA3,TINAGL1,ARRDC2,ANXA9,WDR8,TMEM241,MED15,PRG3,CARD11,RYR1,GAPVD1,EPB41L2,GAPT,POLR1C,GNAI1,NR3C1,NAA25,SMIM22,SCOC,TGM3,CLASP1,HDAC1,SLC9A9,ZEB2,RIC1,NOV,CRISPLD2,CCDC50,IQSEC1,CYP3A43,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,CEP250,VAMP3,GALNS,SLC39A7,TOR2A,NT5E,UST,ZRANB1,OSBPL6,TRIM71,EFR3A,SRPK1,RBM14,NANS,ETV6,VPS52,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,PTDSS1,FBXW11,MIEF2,LOXL1,OGDH,PAM16,MAN1A1,RAB40C,NUP93,ADGRV1,TRIM26,SPPL3,EYA3,SDCCAG8,PLA2G6,BDKRB2,SNAP47,CCDC47,RARG,SECTM1,PLD1,TRRAP,AGAP1,PEBP4,DYRK2,RXRB,APOL3,SPATA24,DMXL1,GALNTL6,STAT4,TRAF1,F5,MAPK1,ST6GALNAC4,WSB1,IQGAP2,RMND5A,WNK1,KATNAL1,PIGV,TMEM123,PHF1,HSD17B12,PMM1,PTPRC,AP2B1,ZC3H14,RANBP3,SPATA5,ARAP1,TUBD1,RNF103-CHMP3,ATOX1,SCARB1,ORAI1,ALOX15,UBASH3B,BCL2,TECR,ABHD12,NOTCH2,SEPHS1,CYB5R3,SMURF2,DTD1,ADGRG6,EPHX1,SHMT2,ADRBK2,ARID4A,PELI1,LIMD1,CHST15,SPIRE1,RAB7A,FMNL1,SPTBN2,ARHGAP10,HLCS,PEX2,FARP2,STX2,IDO1,KRT2,NAA16,EPS8L3,BHLHE40,GPD1,TXNDC11,PIWIL2,CELF2,FYN,RBKS,UPF1,ADAP1,POLR3A,SIAE,THEMIS2,ANKRD11,SPOP,LRIT3,HADH,FAM83A,PPP3R1,STK10,LSG1,KIF6,GID8,RNF13,EPAS1,PER2,ASAP2,WWC2,ERMN,TMEM63A,TRIM29,PIK3CB,GNS,SPECC1,PPP2R5B,CLMN,STAT3,SLAMF1,SYN3,MEF2C,MAP4K5,EEFSEC,PYCR1,ARHGDIB,REEP4,INHBA,HERC1,ANKRD13A,GRK4,CXCR4,TMEM201,DAZAP1,PGM1,IMMT,CEP128,BLVRA,HEXIM1,SPRED2,ETS1,ZNF365,TOM1,PEX11G,COL4A3BP,TAF6,NPPA,MAP4,DNAH3,ARHGAP12,RMDN3,ARFGEF2,MAP3K8,VEGFA,LRCH1,UQCRH,LCLAT1,PLEKHM3,FTL,PRDM16,FAR2,CPEB3,CDK14,TMEM203,APP,GPSM1,SEC62,YARS,RASSF1,CSAD,SLC35C1,IGF2BP2,SENP7,AUTS2,CHSY1,XPO6,RUNX3,PDXDC1,ACOXL,ZFYVE21,LAPTM4A,HBZ,FADS1,RALGPS1,SRP68,DBNL,ADORA1,PLA2G4F,MAST2,GDA,ZBTB16,SYK,MAPKAP1,TIMP2,RFFL,H6PD,AFF3,RIOK2,NTRK1,CDK2,CYSTM1,CHPT1,RPS6KA4,ECHDC1,GPR107,ANXA2,GTPBP2,EIF3M,GNB1,KRT71,FGF1,AGL,ELOVL6,SIK2,DHRS9,JSRP1,SNX10,SHCBP1L,SGK2,ANTXR2,YWHAE,GGNBP2,SLFN14,PHACTR2,KAZN,WDR1,SLA,AKT3,JAZF1,SDC1,DNAJB13,TLE1,PLA2G15,OLA1,GSAP,GNAI2,YES1,EXOC6B,TSPAN33,ITGA2B,EREG,AEBP1,GPC5,RBM19,CPPED1,SMPD3,CORO7-PAM16,MLLT1,CPSF6,CREM,SIAH1,ACVR1B,SPAST,ALKBH5,CALD1,PTK2,C15orf48,AMBRA1,SLC4A1,ERN1,BASP1,RBPJ,RHOA,ESYT3,ARHGEF3,C2CD3,DOCK4,APBB1IP,TOLLIP,IKBKB,PSMD13,TPPP3,FER,KLF7,FANCA,SNUPN,ENPP3,DRC7,CHID1,SETBP1,MRPL10,CAPN10,STUB1,RDH5,CDK19,CAPZA2,ENTPD7,KAT5,CEP85,SIPA1L2,CTSA,PTPRN2,TALDO1,MFSD10,DEDD,FOXO3,CAPN7,FUT4,ELOVL5,APAF1,TUBB,BICC1,PYROXD2,BSCL2,FSCN3,CDCA7,PARN,COL1A1,ATF7,SEC23B,TRAPPC3,NUP210,UCKL1,OTOF,TGFBRAP1,IRF2,TIMM22,GSK3B,YWHAZ,SSTR1,SERGEF,GMEB1,ZC3H4,MAPKAPK2,ORC1,RHOBTB3,PIP5K1C,TRIB2,PDZD2,LRRFIP1,FXR2,LARP4B,USP6NL,CALR,DPP9,CPNE2,MPV17,PALD1,CLCN6,NME2,VTI1B,MRAP,NPM3,PODN,TMCC1,SYNGAP1,TNS3,GPSM2,SLC7A6OS,SARM1,PIK3C2B,PARP15,ARL8B,SMAD2,CDK5,CHD3,ATP1A1,CTLA4,FAH,TAGAP,PGD,UBXN7,MYB,CYP4F12,DNAJB6,ANP32A,COL13A1,CMYA5,CCDC88C,BCL2L1,TGFB1,SFXN5,IQSEC3,DAB2IP,PPARGC1B,LATS2,PLEKHG6,ECHDC3,KLHL3,ADK,IGF2R,CRTC1,MYT1,UBR1,GCNT2,KRT1,NET1,MAPRE2,NEK7,C10orf88,FARP1,STAMBPL1,AMFR,ACSF3,RAB25,UBA7,MCF2L,MYO10,LPCAT1,TTLL11,KTN1,ZDHHC16,SEC14L1,EPB42,LNPEP,GNA12,SEC61A1,RXRA,NOD1,TAOK3,ACADL,NME7,PARD3B,ZMYND10,ZDHHC1,PRKG2,CSNK1G3,FAM110B,TMEM117,DAPP1,ZNF438,EDEM2,XPC,GNA13,ALDH1A2,MYOM1,HNF4A,KANK1,WNT3A,TTC28,UBAP1,KRT6B,ZFAND2A,CXXC5,RNF121,SCTR,FNBP1,RBMS1,TAF15,CERK,STX16,TYSND1,MAFF,WEE1,PPCDC,MYH11,FGD4,FDXACB1,AIF1L,FBXO31,GALNT2,ARHGAP11A,ZFHX3,REPS1,ALDH3B1,PBX1,ATP8B1,SHROOM3,CCR3,KIF21B,CNTRL,PLCG2,GABBR1,VCL,SYNJ1,CNGA4,ADCK1,GDPD3,RPL36AL,CAMTA1,PIGS,ITIH4,MUC1,ATP2B4,CCIN,HERC2,FOXK2,SVIL,PKIG,ARF1,TP53BP1,ASPSCR1,PRKCA,RCC1,GLRX5,ABHD8,MDFIC,CCND3,FTO,MARK2,ATP10B,CLPB,FAM168B,FUCA1,SLC7A8,STRN4,SV2B,BTRC,CHMP4B,UPF3A,GET4,NFASC,GRK5,TBC1D14,RASAL2,COG7,TEX2,NDUFV2,CDH15,AGPAT3,SHB,HPS1,ATP8B2,STX17,CNPY3,XPNPEP3,SORBS2,PDZRN3,DCTN2,TPST2,BATF,GEMIN5,RDM1,MYO1A,SLC39A1,RHBDD1,FCRLB,FDFT1,PARP4,GLE1,GSTM4,NEK6,BRCA1,DEGS2,ITGB5,MNDA,SERPINB6,TTLL4,NLRX1,PSMB7,SGK1,METTL8,RAB11FIP3,ACSM6,NRROS,STXBP2,OSBPL8,STAT5B,PNPLA2,NCAPH,URM1,TNRC6B,RPUSD3,SMAD3,SLC23A1,FOXO1,SMG9,RGL1,LIG3,SORL1,TRPM2,RSU1,NFE2,DCTN5,MFSD12,TAF5L,LHFPL2,FNTB,ZKSCAN3,AOAH,CRYM,NDUFA4,ATP6V0A2,PIEZO1,SAMD8,MT2A,CLEC16A,HIBADH,MX1,TRAK2,FURIN,UNK,WWP1,SLC25A13,UGT1A7,SNTB1,RAB7L1,FRYL,ARPC4,KRT31,RBM44,TEC,FANCC,SMAD5,ANXA4,SIRPA,SV2C,RAD23A,SLC8A3,PPP1R12B,RYR3,SUMF1,IRS2,NBEA,TACC1,CSRP3,CLIC5,PEX11A,INPP1,ACSL6,STARD10,THUMPD3,POU2F1,IRS1,SFMBT2,LCK,SPOCK1,UBE2K,TGFBR2,TULP4,RAB11FIP2,JARID2,JAKMIP2,EEF1G,ARIH2,NRF1,LGALS3,EIF4A3,SH3BP1,KCTD1,TUT1,PPM1L,NUSAP1,EHD4,LEPROTL1,ITPR2,EXOC4,FEM1C,RNF145,DCUN1D1,ZBTB7A,USP46,DHRS4,MYO5A,FAM174B,FBN1,RET,DUS2,RNF11,CHCHD6,DNAJA3,ARHGEF4,MDM1,CCAR1,REXO2,ARHGAP35,ANP32B,TMEM130,ASL,SHANK2,THRSP,DLK1,ZBTB20,MKNK1,IRF7,MAT2B,HSPG2,PRIMPOL,BNIP3L,ATP6V1H,ST6GAL1,RHEB,VAC14,CACNA1C,TTC3,ATP9A,KIF13B,STK24,BET1L,ANKRD6,FLT3,WDR37,ZNF638,SLC30A1,RRBP1,GLUL,ANKS6,PIGR,PDE7A,TRAPPC12,SLC27A3,DHX8,SLC8B1,VRK1,PARP16,KCNE2,EDARADD,RSPRY1,NLK,FSTL4,PRKCQ,SLC38A10,TNFAIP1,CERKL,PPIC,UBXN4,STAU1,BRD8,SLC35E4,WDR11,DBF4B,FNIP2,PLD4,LUZP6,HIF1AN,BAG2,KIF5B,ARMC8,TUBGCP3,FKBP5,BCAS3,DDHD1,DACH1,DERA,PDE8A,CABLES1,SCAF8,DCLK3,UTRN,CSRP2BP,ATP2A2,STK11IP,FRY,MDN1,AKT2,ARMC4,PRDX3,MPL,DCP2,SIN3B,HRK,C6orf89,PARP10,MCFD2,URGCP,CCDC141,NEIL2,FGF18,CD58,TRIM2,TRAM2,FNIP1,TP53BP2,ADAMTS7,LAPTM4B,FAM91A1,MOB1A,CLYBL,IVNS1ABP,RALGPS2,ARSK,SRSF7,RAB3IL1,SGPP1,PARP1,NCAPD2,TTBK2,SLC4A8,ACTRT2,CYBRD1,NTAN1,FARS2,MFF,SPPL2B,FRMD4B,TMEM79,SLC37A1,ARMC9,PRDM2,CAT,OSBPL10,FBXW7,MERTK,HNF1A,PSMD1,SCG3,CDC25C,MTSS1,UBASH3A,SNX4,CRLF3,ZC3H12C,SGIP1,STAT6,PRDM1,ZDHHC17,PPP6R3,GIGYF2,TMOD2,TP73,ITGB1,TNFAIP8L3,STEAP3,TPT1,HIP1,CDKAL1,SPSB4,HS6ST1,NECAB1,EZR,AHI1,TMEM64,CTSS,STARD3,DUT,GNPNAT1,CCDC96,SPATA16,RNF130,ARHGEF10L,PLA2G4A,HYAL2,ATG16L1,ICA1,MTA1,PADI6,CLTC,KIF13A,BBX,TNIP2,MYLIP,SPEF1,SLC25A38,RPGRIP1,MAMDC2,SLC11A2,DENND1B,NDUFB9,HAL,LYN,CENPJ,SERBP1,GAS2L1,ACP6,VWA3B,AKT1,ACR,GRAMD4,UBTD2,UBXN1,UNC50,KPNA4,SLC1A3,ATXN7,PEX14,PDE4C,MAPK6,DOK4,MOSPD3,TFB1M,ST3GAL6,ZADH2,HIPK3,METTL1,LTC4S,CASKIN2,GULP1,PPTC7,CARD14,ALS2,DTNA,ZNRF2,INPP5D,RAPGEF3,ROR1,ACLY,BTBD1,TBC1D10B,NPHP1,LAPTM5,BIRC6,CLCC1,A3GALT2,NCOA2,ACTB,PIGC,TOP2B,BAIAP2,SCRN1,BRIP1,TFG,CAST,HMCN1,NDST1,WT1,ST3GAL5,ATG10,COPA,ARHGAP9,FBXW4,DNAJC5,CEP83,TSNAXIP1,CSNK1G2,RPS15A,ASB2,CLEC12A,DST,CLSTN1,PSMG1,ANKRD13B,LETM1,LPIN2,PHB2,PDLIM2,BUB3,NACC1,LITAF,MYO1F,WBP2,MRM1,SURF4,HOOK1,COG3,LMAN1,GNG5,HEATR5A,SEC24A,DIXDC1,MDGA1,SFI1,LIPC,HCLS1,ERN2,MAP2K6,CREB3L1,FBXO9,IL10RA,LRCH3,PCSK5,CYB5B,SH3GLB2,IFITM1,FLNB,NDUFS6,RABGAP1L,PKD2,USP1,NARS2,MSRA,ATL1,ZMIZ1,DRD2,CD47,EFR3B,SNX20,GAS2,CERS6,IFIT2,MLLT3,ACSL5,EXOC5,TFCP2,C1GALT1,PPP2CB,PEX7,ARAP3,PLAA,IL15,ARNT,NEURL1B,SERPINF1,SLC25A10,TMEM168,CPA3,PGAP2,JPH2,DNAJC13,RAB27A,MRPL55,CREB3L3,BRD7,ATAD3C,MIA3,TRIM62,GMPPB,ARID4B,PFKFB4,CEP295,ALOX5,COQ5,CIT,PIN1,INSR,CCDC181,NCOA4,CANX,NCK1,EIF4H,DCAF5,HIPK1,PRUNE2,CA4,EIF4G3,OAT,MGST2,FYCO1,MICU1,RBFOX2,DCTN4,PEAK1,FLOT1,CAND2,SPAG4,YOD1,NOX3,APLF,LIMCH1,GLYCTK,CNKSR3,ZDHHC14,TSPAN14,STAU2,NFE2L1,DGAT2,DLC1,ATXN10,ALOX12B,MYRFL,OTULIN,PRR5,YY1AP1,PPP2R1A,TMEM50B,DYM,MCCC1,KPNB1,KCNN3,B3GALNT1,NUDT19,GPRC5A,ALDH6A1,GALNT11,CDYL,ACVR2A,DBN1,HSPD1,HMOX2,COLGALT2,HIVEP3,TBC1D13,MAP3K4,NAPG,EDEM3,CARS,RAB8B,CHST3,RAP1A,TNPO1,MTF1,FGD5,RASGRP3,PSEN1,MRPL16,SGSM2,AHRR,TP63,PPP2R5D,ASTL,CFAP36,NBAS,CPEB4,LAMA3,TEX14,PPP1CA,SEC63,FDX1,MPRIP,REEP5,ITFG2,NGLY1,USP47,SPIRE2,SPTLC2,KLHL5,GPS2,ZEB1,WDR7,SEMA6D,MMP28,GMDS,PGS1,TMEM39A,PIK3R2,ANKRD28,FASTKD2,AAGAB,RNF19A,CPT1A,SEMA4C,GSPT1,QKI,ARL2,ALG14,FKBP1B,MRPS14,BATF3,IQGAP1,AMPD2,AFTPH,ACIN1,TOR1B,HBS1L,ANKRD9,NCAM1,ATF6,INPP5E,PDPK1,SLC25A44,MAP2K3,PLCB1,GALNT18,ADD3,BIK,NUCKS1,ELP6,PACS2,MON2,ALAD,PANK1,CCDC146,EXTL1,RPS6KA1,NEK1,NMNAT1,KIF3B,SUFU,STX1B,CNST,VPS26B,MDM2,NFKBIB,LRRC61,PLCB2,PITPNA,ESYT2,SLC40A1,GALK2,ZFAND6,RASA2,RB1CC1,SCG5,DFFA,C17orf62,PKNOX1,ST8SIA6,RCBTB2,COG2,RUNX2,NCLN,PAK2,ALAS1,FLT1,CLCN7,DOCK10,EMID1,GCNT3,C1orf9,PRKAR2A,PCM1,RNASET2,MTMR7,ZFAT,CLNS1A,ASAH1,TIAM2,RRAS2,FAM49B,TRIP4,MKRN1,UNC119,MARK4,NAGLU,DHX33,SDCBP2,PIK3R3,GLRB,ASB3,MAP3K5,MEOX1,ATP6V0D1,ZMYND8,BCAS4,KLHDC3,HSPB1,SORBS1,TXNDC2,PIKFYVE,CAMK4## [1] 5554 8write.table(gem, file=file.path(res.dir,
paste0("gProfiler2_cra_camp_logIgE_DMPs_enrich_hypo_", timeStamp, ".txt")),
sep="\t", quote=F, row.names=F)
table(gem$Domain)##
## CORUM GO:BP GO:CC GO:MF HP HPA KEGG MIRNA REAC WP
## 1 1559 263 207 1169 409 167 1287 309 183path.hypo <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hypo)## [1] 659 8#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hypo, filter = 'top')# do the above steps again after restriction on effect size and genome-wide threshold of 5.8e-08
uniq.hyper <- merge_CG[merge_CG$Direction_camp_cra=="++",]
uniq.hypo <- merge_CG[merge_CG$Direction_camp_cra=="--",]
# Idea was that highest betas sometimes are at top but looks like that
# isn't the case here so I am not restricting by effect size for now
hyper.hist.cra <- ggplot(uniq.hyper) + geom_histogram(aes(beta_coeff_cra), bins=50) + labs(x="Hypermeth betas distribution CRA")
hyper.hist.camp <- ggplot(uniq.hyper) + geom_histogram(aes(logFC), bins=50) + labs(x="Hypermeth betas distribution CAMP")
hypo.hist.cra <- ggplot(uniq.hypo) + geom_histogram(aes(beta_coeff_cra), bins=50) + labs(x="Hypometh betas distribution CRA")
hypo.hist.camp <- ggplot(uniq.hypo) + geom_histogram(aes(logFC), bins=50) + labs(x="Hypometh betas distribution CAMP")
p <- grid.arrange(hyper.hist.cra,hyper.hist.camp,hypo.hist.cra, hypo.hist.camp, nrow = 2, ncol = 2)
ggsave(p, file=file.path(sub.plots.dir,
"hist_hyper_hypo_cra_camp_betas.png"), width = 9, height = 9)
####################################
# Filter by genome-wide threshold
####################################
merge_CG_gw <- merge_CG[merge_CG$P.Value_cra<5.8e-08 & merge_CG$P.Value<5.8e-08,]
dim(merge_CG_gw)## [1] 2865 62uniq.hyper <- merge_CG_gw[merge_CG_gw$Direction_camp_cra=="++",]
uniq.hyper <- unique(uniq.hyper$Gene.x)
uniq.hyper <- uniq.hyper[uniq.hyper!="NA"]
uniq.hyper <- uniq.hyper[uniq.hyper!=""]
length(uniq.hyper) # 214## [1] 214uniq.hypo <- merge_CG_gw[merge_CG_gw$Direction_camp_cra=="--",]
uniq.hypo <- unique(uniq.hypo$Gene.x)
uniq.hypo <- uniq.hypo[uniq.hypo!="NA"]
uniq.hypo <- uniq.hypo[uniq.hypo!=""]
length(uniq.hypo) # 1,332## [1] 1332enrich.hyper <- gprofiler2::gost(query=uniq.hyper, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))## Detected custom background input, domain scope is set to 'custom'names(enrich.hyper)## [1] "result" "meta"# Results containing all annotated terms for hyper-methylated CpGs
gem <- enrich.hyper$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
head(gem); dim(gem)## GO.ID Description term_size intersection_size
## 317 GO:0005737 cytoplasm 11268 146
## 730 MIRNA:000000 MIRNA root 14165 163
## 464 HPA:0530000 spleen 5539 86
## 378 GO:0005488 binding 15946 174
## 318 GO:0005622 intracellular anatomical structure 13844 158
## 465 HPA:0530711 spleen; cells in red pulp[≥Low] 5000 78
## Domain FDR Phenotype
## 317 GO:CC 1.278093e-09 +1
## 730 MIRNA 1.034643e-06 +1
## 464 HPA 1.412058e-06 +1
## 378 GO:MF 1.466783e-06 +1
## 318 GO:CC 1.893883e-06 +1
## 465 HPA 5.501473e-06 +1
## Genes
## 317 TFR2,ZMIZ1,TGFBR2,GSG1,RBKS,KIF5C,XYLT1,ABL1,RUFY4,CARS,ATN1,GALNT6,CELF2,COL23A1,UCK2,AZU1,VAV2,DAAM1,KIF13B,TARM1,ASB1,LPP,MGAT5,CAMKK2,POC1B,DTNB,TPP1,SERGEF,KIAA0319L,APP,GNG7,CAMK2G,NLRC4,CHST11,TERF2,PREX1,PRKAG2,MPO,SORCS2,WDFY4,VDR,TOR3A,TRIM67,LIPC,SSH1,WDFY1,SVIL,DENND2D,PRKCH,PSMB7,GM2A,SSH2,MOK,FAM193B,ZDHHC14,PPM1H,LRRK1,TTC7A,SLPI,ZNF148,TGFBI,LTF,ATPAF2,TNS1,KLHL25,GALNT14,ACOXL,CLEC5A,GLIPR2,OPRM1,NEDD9,MKNK1,NISCH,CAMK1D,NGF,RBSN,EPB41L3,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,ADAM19,KIDINS220,RHBDF2,CUX1,SPARC,KIAA0586,DYM,TNF,RPTOR,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,DEFA4,PPP2R5C,EFR3B,TNS3,GDI2,ARRDC5,MARCO,FCN1,AFAP1,SLC25A37,TRIM27,JARID2,DYNC1H1,MTAP,MYO18A,PCK2,SIRPA,FKBP15,SYNJ2,ABCA13,CCRL2,UBASH3B,TMEM150B,CRYL1,MIF4GD,TGOLN2,PIK3C2B,VTI1A,CREB3L4,ITPR2,HIPK3,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,LITAF,TNFRSF1B,KCNAB2,SDCCAG8,AP1G1
## 730 ZMIZ1,TGFBR2,C20orf27,GSG1,KIF5C,TREM2,XYLT1,ABL1,SLC7A7,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,LRRC27,UCK2,VAV2,DAAM1,KIF13B,ASB1,PCGF3,LPP,MGAT5,CAMKK2,KIAA1549L,DHX57,POC1B,DTNB,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,FBN2,CAMK2G,NLRC4,LYPD4,CHST11,TERF2,PREX1,MPO,SLX4IP,POLE,SORCS2,WDFY4,VDR,TOR3A,TRIM67,LIPC,SSH1,MACROD1,WDFY1,SVIL,DENND2D,PRKCH,PSMB7,GM2A,INTS6,SSH2,FAM193B,ZDHHC14,PPM1H,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,TNS1,IFFO2,KLHL25,GALNT14,CLEC5A,GLIPR2,OPRM1,NEDD9,MKNK1,CACNA2D2,NISCH,CAMK1D,RBSN,SSBP3,EPB41L3,CPM,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,ADAM19,KIDINS220,CYB561D1,RHBDF2,CUX1,SPARC,KIAA0586,DYM,TNF,RPTOR,CCDC149,UBN1,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,DEFA4,GPX3,HLX,PPP2R5C,EFR3B,TNS3,GDI2,RBM20,FAM168A,AFAP1,SLC25A37,TRIM27,JARID2,DYNC1H1,MTAP,MYO18A,PCK2,SIRPA,PCOLCE2,FKBP15,SYNJ2,GATAD2A,ABCA13,CCRL2,UBASH3B,IL18RAP,CRYL1,MIF4GD,TGOLN2,PIK3C2B,VTI1A,ITPR2,HIPK3,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,ADCY9,LITAF,TNFRSF1B,NAV3,VIT,SDCCAG8,AP1G1,NID1
## 464 TREM2,XYLT1,ABL1,CARS,ATN1,NCOR2,GALNT6,CELF2,AZU1,PCGF3,MGAT5,CAMKK2,TPP1,SERGEF,CHST11,TERF2,PREX1,TOR3A,WDFY1,SVIL,DENND2D,PRKCH,PSMB7,GM2A,INTS6,FAM193B,PPM1H,TTC7A,ZNF148,LTF,ATPAF2,TNS1,IFFO2,KLHL25,GLIPR2,MKNK1,NISCH,PTX4,RBSN,PRDX5,TMEM8B,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,KIDINS220,CUX1,SPARC,DYM,TNF,RPTOR,TPD52L2,PCNT,FKBP9,DEFA4,PPP2R5C,GDI2,FCN1,AFAP1,TRIM27,JARID2,DYNC1H1,MYO18A,SIRPA,FKBP15,SYNJ2,GATAD2A,CCRL2,UBASH3B,IL18RAP,MIF4GD,TGOLN2,VTI1A,CREB3L4,HIPK3,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,ADCY9,LITAF,KCNAB2,SDCCAG8,AP1G1
## 378 TFR2,ZMIZ1,TGFBR2,C20orf27,GSG1,RBKS,KIF5C,TREM2,XYLT1,ABL1,RUFY4,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,LRRC27,UCK2,AZU1,VAV2,DAAM1,KIF13B,TARM1,ASB1,PCGF3,LPP,MGAT5,CAMKK2,DHX57,POC1B,DTNB,TPP1,SMYD4,SERGEF,KIAA0319L,APP,GNG7,FBN2,CAMK2G,NLRC4,TERF2,PREX1,PRKAG2,MPO,SLX4IP,POLE,SORCS2,WDFY4,VDR,TOR3A,TRIM67,LIPC,SSH1,MACROD1,WDFY1,SVIL,TNN,DENND2D,PRKCH,PSMB7,INTS6,SSH2,MOK,FAM193B,PPM1H,LRRK1,TTC7A,ADGB,SLPI,ZNF148,TGFBI,LTF,ATPAF2,TNS1,KLHL25,GALNT14,ACOXL,CLEC5A,GLIPR2,OPRM1,SLC10A1,NEDD9,MKNK1,CACNA2D2,NISCH,PTX4,CAMK1D,NGF,RBSN,SSBP3,EPB41L3,CPM,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,ADAM19,KIDINS220,CYB561D1,RHBDF2,CUX1,SPARC,DYM,TNF,RPTOR,UBN1,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,DEFA4,GPX3,HLX,PPP2R5C,EFR3B,MIR145,TNS3,GDI2,RBM20,ARRDC5,MARCO,FAM168A,FCN1,AFAP1,SLC25A37,TRIM27,JARID2,DYNC1H1,MTAP,MYO18A,PCK2,SIRPA,PCOLCE2,FKBP15,SYNJ2,GATAD2A,ABCA13,CCRL2,UBASH3B,IL18RAP,CRYL1,MIF4GD,TGOLN2,PIK3C2B,VTI1A,CREB3L4,ITPR2,HIPK3,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,ADCY9,LITAF,TNFRSF1B,KCNAB2,NAV3,VIT,SDCCAG8,AP1G1,NID1
## 318 TFR2,ZMIZ1,TGFBR2,GSG1,RBKS,KIF5C,XYLT1,ABL1,RUFY4,CARS,ATN1,NCOR2,GALNT6,CELF2,COL23A1,UCK2,AZU1,VAV2,DAAM1,KIF13B,TARM1,ASB1,PCGF3,LPP,MGAT5,CAMKK2,POC1B,DTNB,TPP1,SERGEF,KIAA0319L,APP,GNG7,CAMK2G,NLRC4,CHST11,TERF2,PREX1,PRKAG2,MPO,POLE,SORCS2,WDFY4,VDR,TOR3A,TRIM67,LIPC,SSH1,MACROD1,WDFY1,SVIL,DENND2D,PRKCH,PSMB7,GM2A,INTS6,SSH2,MOK,FAM193B,ZDHHC14,PPM1H,LRRK1,TTC7A,SLPI,ZNF148,TGFBI,LTF,ATPAF2,TNS1,IFFO2,KLHL25,GALNT14,ACOXL,CLEC5A,GLIPR2,OPRM1,NEDD9,MKNK1,NISCH,CAMK1D,NGF,RBSN,SSBP3,EPB41L3,SUFU,PRDX5,IGHMBP2,TUT1,TMEM8B,CYP19A1,ZNF438,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,ADAM19,KIDINS220,RHBDF2,CUX1,SPARC,KIAA0586,DYM,TNF,RPTOR,UBN1,TPD52L2,ABCC11,ROPN1L,PCNT,RALGAPA2,IRAK2,FKBP9,DEFA4,HLX,PPP2R5C,EFR3B,TNS3,GDI2,RBM20,ARRDC5,MARCO,FCN1,AFAP1,SLC25A37,TRIM27,JARID2,DYNC1H1,MTAP,MYO18A,PCK2,SIRPA,FKBP15,SYNJ2,GATAD2A,ABCA13,CCRL2,UBASH3B,TMEM150B,CRYL1,MIF4GD,TGOLN2,PIK3C2B,VTI1A,CREB3L4,ITPR2,HIPK3,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,LITAF,TNFRSF1B,KCNAB2,NAV3,SDCCAG8,AP1G1
## 465 TREM2,XYLT1,ABL1,CARS,ATN1,NCOR2,GALNT6,CELF2,AZU1,PCGF3,MGAT5,CAMKK2,TPP1,CHST11,TERF2,PREX1,WDFY1,SVIL,DENND2D,PRKCH,GM2A,FAM193B,PPM1H,TTC7A,ZNF148,LTF,ATPAF2,TNS1,IFFO2,KLHL25,GLIPR2,MKNK1,NISCH,PTX4,RBSN,PRDX5,TMEM8B,ANKRD11,ACACA,ARHGEF10,ME3,HSD17B12,KIDINS220,CUX1,SPARC,DYM,TNF,RPTOR,TPD52L2,PCNT,FKBP9,DEFA4,PPP2R5C,GDI2,FCN1,AFAP1,JARID2,DYNC1H1,MYO18A,SIRPA,FKBP15,SYNJ2,GATAD2A,CCRL2,UBASH3B,IL18RAP,TGOLN2,CREB3L4,KIF21B,ETV6,SEPT9,HDAC4,LRRFIP1,ADCY9,LITAF,KCNAB2,SDCCAG8,AP1G1## [1] 745 8write.table(gem, file=file.path(res.dir,
paste0("gProfiler2_cra_camp_logIgE_DMPs_enrich_hyper_gwthresh_", timeStamp, ".txt")),
sep="\t", quote=F, row.names=F)
table(gem$Domain)##
## CORUM GO:BP GO:CC GO:MF HP HPA KEGG MIRNA REAC WP
## 96 220 61 41 45 258 8 4 11 1path.hyper.gw <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hyper.gw)## [1] 20 8#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hyper.gw, filter = 'top')enrich.hypo <- gprofiler2::gost(query=uniq.hypo, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))## Detected custom background input, domain scope is set to 'custom'# for results containing all annotated terms
gem <- enrich.hypo$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
head(gem); dim(gem)## GO.ID Description term_size
## 2254 MIRNA:000000 MIRNA root 14165
## 958 GO:0005737 cytoplasm 11268
## 1124 GO:0003674 molecular_function 17356
## 1125 GO:0005515 protein binding 13924
## 1126 GO:0005488 binding 15946
## 959 GO:0005622 intracellular anatomical structure 13844
## intersection_size Domain FDR Phenotype
## 2254 1042 MIRNA 1.267017e-66 +1
## 958 879 GO:CC 4.864073e-54 +1
## 1124 1144 GO:MF 7.088657e-54 +1
## 1125 1006 GO:MF 7.088657e-54 +1
## 1126 1091 GO:MF 8.698490e-54 +1
## 959 1001 GO:CC 1.614487e-53 +1
## Genes
## 2254 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,TTC7A,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,NHLRC4,KIAA1522,GNB5,TMED3,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,SLC29A1,EHD1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,ELMO1,GPR176,FBXW8,MITF,SLC25A33,ABCC1,SLC7A1,TNIK,TRIM9,DAPK2,TFF2,GFOD1,IL5RA,OSBPL5,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,IL4,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,SLC2A8,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,PNN,SLC24A3,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CBFB,EPHB2,TTYH3,CHP1,VPS53,ZNF48,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,C6orf132,ERMAP,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,ITGAL,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,SLC45A4,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,TRIM33,UBE3B,HEXA,MTMR3,SH3GL1,NCOR2,ENTPD1,SLCO3A1,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,GALNT10,NVL,POR,AXIN1,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,ADORA3,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,CCDC127,HK2,DYRK1A,MLX,BATF2,DAG1,KRT8,LGALS8,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,PLXNA2,ANKRD52,SERINC5,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,P2RY2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,BACH1,MAP6D1,C11orf24,DPH7,ACSL1,ABR,DOCK1,BCAS1,NEMF,RAB11FIP1,MAP1LC3B2,BDH1,FHL2,CMBL,TANGO2,ELMO2,COL15A1,SLC2A9,GJB3,SGMS1,SPATS2L,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,SLC41A1,SSBP3,FOXJ3,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,AQP1,GPR156,DENND3,FCHSD2,CDH1,TMEM86B,FBXO7,ABCB9,CCDC85C,GRAMD1B,CALML4,PELI2,PHLDB3,SIAH2,MICAL2,TMOD3,SAP30L,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,ZNF70,IL13,CCNY,DMAP1,SLC23A2,RREB1,PSTPIP2,TMEM154,ABCC4,ADAMTS14,PDE4B,GNG12,PI4KA,NADK,ZC3H11A,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,RNF40,ZKSCAN5,RBL2,GSN,TRAF3,LTBP4,SEMA3B,TPCN1,MCM2,CAB39,GALM,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,THYN1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,NCK2,RNF157,IKZF1,SULF2,GSTM3,TGFA,GALNT12,CEBPB,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,FAM53B,SPTBN1,MYL9,GLB1,TNXB,DENND5A,ST3GAL1,XYLT1,SOAT2,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,SOGA1,ZNF532,EML3,ZSWIM3,SNX9,LRRN2,BCL7A,MCMBP,DNAJC3,WNT3,GALNT7,UXS1,MTUS2,DHCR24,PHF13,C19orf54,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,TMEM116,NFATC2,ZHX2,TMEM104,NXF1,SLC2A6,CACNA2D1,NELFCD,ABHD2,TESPA1,TOPBP1,PACSIN2,PIGN,CDKN2AIPNL,WDFY2,AGAP3,MAML1,EFNB2,ATG13,PHTF2,LARP1,TBC1D9B,CACNA1D,STK3,KBTBD4,CHRNE,LRRC8C,P2RX7,PIK3AP1,LINC00548,P3H2,VPS13D,OSBPL3,ASNSD1,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,NBPF8,STON1-GTF2A1L,PLLP,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,JAG1,XAF1,ERG,NEDD4L,VAMP1,AGXT,NAP1L4,GTPBP1,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,IL34,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,SECISBP2L,MBD6,RCC2,PAFAH2,SLC45A3,SLIT3,USP19,IL18BP,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,COL4A1,ARL15,SELPLG,LEF1,LRRC20,RIBC2,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,B3GALNT2,THADA,ELL2,RAPGEF1,HDAC4,EXT1,ACTN4,GPD2,C16orf45,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,HNRNPM,SIPA1L3,RMND1,ARL6IP4,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,PTPN1,UNC5B,AAK1,CDK5RAP3,FBXL2,RAB3B,ZXDC,ABAT,ANO6,INPP5A,IKZF2,CD81,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,RALY,DIDO1,ZNF175,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,ATP2C1,EHBP1,CHCHD3,ARSB,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,TMEM156,DHX37,MVB12A,CLK3,TBC1D2,ZDHHC18,ARHGAP18,EIF4G2,PELP1,CHST11,DGKG,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,MTA2,SIL1,LSM14A,INSC,MYO9B,MYLK4,ERI3,RNF24,CD4,TLE4,TTC17,USPL1,ZBTB34,TMED10,LGR6,LAX1,AACS,MICAL1,ACAD8,MRPS27,TRPV6,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,FNDC3B,ERAP2,ODC1,FBXO34,YWHAQ,CSDE1,COLQ,RBM33,CRABP2,SLC36A1,RSAD2,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,PLEKHA7,MDM4,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,SERF2,UGGT1,EXD2,SMG5,EARS2,TESK2,ACSF2,SPNS3,SCAF11,SRC,PCBP2,SHBG,MTHFD2,TBXAS1,CRTC3,SPI1,UBE4A,LAIR1,OBSL1,SLC12A4,CD151,DHX15,LRRC59,EXOC3,DGAT1,LPP,ARHGEF18,NDUFV1,CD28,PPP2R5E,RFC3,NACC2,CAMP,RASSF5,TMEM41A,HDAC9,SLC44A4,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,FAIM2,RAD21,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,DEPDC1B,MYLK,HIPK2,SAG,ILKAP,EEF2K,TRPM4,NCOA7,ASH2L,EPS15,CMTR1,ART3,WNT5B,TNFAIP8,CSGALNACT1,HMGXB4,SLMAP,PTP4A2,AGPS,FMO1,KIAA0100,ST3GAL2,BICD1,CDC42BPB,AHCYL2,CUX1,LHPP,MUC20,TMEM220,AKR1E2,PSMC1,MCC,WDFY4,USP7,RPRD1A,EFHD2,SPIDR,MAP3K14,BANK1,WDR70,AP1M1,SLC2A5,TMEM51,TRAPPC10,LONRF2,MTA3,GOLGA3,HNRNPLL,WDR8,PRG3,HECTD4,GAPVD1,EPB41L2,POLR1C,GSE1,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,CRISPLD2,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,UST,ZRANB1,OSBPL6,EFR3A,SRPK1,AGER,MTURN,YEATS2,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,PTDSS1,TXNRD2,OGDH,PAM16,TRIM26,SLC22A23,SPPL3,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,REV1,PEBP4,DYRK2,RNF43,LDB2,DMXL1,GALNTL6,STAT4,TRAF1,F5,ST6GALNAC4,WNK1,BAZ1A,HSD17B12,PTPRC,AP2B1,C6orf47,ZC3H14,SPATA5,POLR1A,TUBD1,RNF103-CHMP3,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,VANGL1,ADRBK2,ARID4A,LIMD1,CHST15,TCF7,ARHGAP10,PEX2,IDO1,NAA16,PIWIL2,CELF2,FYN,ARPP19,ABTB2,MED13L,SPOP,STK10,CEBPE,EPAS1,WWC2,ERMN,ARL6IP6,TMEM63A,EIF1AD,PIK3CB,RAB19,STAT3,EEFSEC,HERC1,ANKRD13A,GRK4,SUPT3H,TIGD1,TMEM201,DAZAP1,PGM1,CEP128,BLVRA,SPRED2
## 958 ACOT7,SEC31B,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,PTAFR,GUSB,MSMP,GNB5,TMED3,EVL,AKAP1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,TET3,FBP1,ELMO1,FBXW8,MITF,SLC25A33,TNIK,TRIM9,PRG2,DAPK2,OSBPL5,XXYLT1,TRIM4,UBE2O,ARID3A,SLC25A26,RECQL5,SEC16B,PLD3,MGLL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,ACOX1,ATG14,NENF,SMURF1,RNF220,VKORC1L1,DDC,MFHAS1,PTPRS,ADARB1,TMEM11,KCNH2,AREL1,EPB41,CAPG,NGFR,SLC2A8,HMBS,NDST2,PCSK6,NOLC1,MINK1,CLC,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,UQCC1,HORMAD2,MAP3K7CL,CCM2,EPHB2,CHP1,VPS53,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,ERMAP,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,MYRIP,ITGAL,VTI1A,SYNDIG1,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,HHAT,GALNT6,TBC1D5,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,HEXA,MTMR3,TFR2,SH3GL1,GGCX,NDOR1,PDCL,BCKDHA,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,SLC39A4,POR,AXIN1,RD3,ITPR1,CREG1,DEPDC5,CSNK1D,MTCL1,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,SERPINC1,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,RNF122,PRKCB,GALNT16,MAP3K1,PNPLA1,CACNA1S,PI4KB,GYG1,HK2,DYRK1A,MLX,DAG1,KRT8,LGALS8,WIPI1,URI1,UBXN11,AMPD3,SWAP70,CEL,TVP23B,BIN3,CMTM6,CSRP1,GFPT2,DICER1,QRICH2,SERINC5,ITSN1,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,FADD,SERPINB2,KCNE3,DLG5,PTK2B,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,SAFB2,ACSL1,ABR,DOCK1,BCAS1,RAB11FIP1,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,TANGO2,ELMO2,COL15A1,GJB3,SGMS1,SPATS2L,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,CLRN1,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,PDLIM7,APTX,SLC17A4,CS,UBAC2,NAPB,PTPRJ,CORO1C,MFSD2A,ASAP1,PICALM,GNAQ,ADAM8,FZR1,MED27,AQP1,DENND3,FCHSD2,CDH1,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,PELI2,UPK3A,SIAH2,TMOD3,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,IL13,CCNY,DMAP1,SLC23A2,RREB1,PSTPIP2,HCFC1R1,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,PROZ,USP20,TAF4B,RPS6KA2,LRSAM1,RNF40,AK8,RBL2,GSN,HCK,TRAF3,SEMA3B,TPCN1,MCM2,CAB39,GALM,MAP6,PPP1R1B,TOM1L2,NCALD,FECH,RNF10,FOXK1,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,NCK2,ST3GAL4,RNF157,IKZF1,SULF2,GSTM3,TGFA,GALNT12,CEBPB,ARID1B,KPNA1,CAPZB,GNG7,TRIM8,CCSER2,MIB1,C6orf106,HPD,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,SPTBN1,MYL9,GLB1,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,SOAT2,MAN1C1,POLR3E,METTL16,RAP1GAP2,COL20A1,RASSF2,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,RASSF3,EML3,SNX9,MCMBP,DNAJC3,WNT3,GALNT7,UXS1,MTUS2,DHCR24,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,ABHD2,TESPA1,TOPBP1,PACSIN2,PIGN,SERP2,WDFY2,TBC1D10A,AGAP3,ATG13,PHTF2,LARP1,CACNA1D,STK3,LRRC8C,P2RX7,PIK3AP1,P3H2,OSBPL3,SEPT9,CAPN2,DENND2D,RNF41,COL11A2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,CALR3,STON1-GTF2A1L,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,XAF1,ERG,NEDD4L,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,CLDN10,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,RCC2,PAFAH2,SLIT3,USP19,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,RALBP1,RIC8B,PHACTR1,COL4A1,WWOX,NAPA,LEF1,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,CREB3L2,NIPSNAP3B,ATP2A3,AHNAK,DNAH1,B3GALNT2,HNMT,THADA,RAPGEF1,AGBL4,IL16,HDAC4,EXT1,ACTN4,GPD2,ENO3,XPR1,RBPMS,ARSG,RASGRP1,HNRNPM,SIPA1L3,RMND1,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,SRGAP3,PTPN1,AAK1,BEST1,CDK5RAP3,FBXL2,RAB3B,ABAT,ANO6,PIK3R5,TMOD1,MAP2K5,UBE2D3,ALDH2,DIDO1,ZNF175,PARP9,CLSTN3,PHKB,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,ATP2C1,EHBP1,CHCHD3,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,DHX37,MVB12A,CLK3,TBC1D2,ZDHHC18,KCNAB2,ARHGAP18,EIF4G2,PELP1,CHST11,P4HTM,DGKG,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,SIL1,LSM14A,INSC,MYO9B,RNF24,CD4,DNAH2,TTC17,TMED10,LGR6,PDE9A,LAX1,AACS,MICAL1,ACAD8,MRPS27,PIGL,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,ERAP2,ODC1,RAB20,YWHAQ,CSDE1,CRABP2,SLC36A1,RSAD2,TKT,PTEN,PRKAB1,KDELC2,ADD1,PLEKHA7,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SARNP,TESK2,ACSF2,SRC,PCBP2,C20orf203,MTHFD2,TBXAS1,CRTC3,UBE4A,LAIR1,OBSL1,SLC12A4,CCBL1,CD151,LRRC59,EXOC3,DGAT1,LPP,ARHGAP24,ARHGEF18,NDUFV1,CD28,PPP2R5E,NACC2,CAMP,RASSF5,CLTCL1,HDAC9,EPHA4,GLIPR2,MCU,MLXIP,NBPF20,KCNA2,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,UPP2,ARHGEF7,SYTL3,FAIM2,RAD21,SPECC1L-ADORA2A,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,DEPDC1B,MYLK,HIPK2,SAG,ILKAP,EEF2K,TRPM4,EPS15,CMTR1,WNT5B,TNFAIP8,CSGALNACT1,SLMAP,PTP4A2,AGPS,FMO1,ST3GAL2,BICD1,CDC42BPB,AHCYL2,CUX1,LHPP,MUC20,TXNDC8,AKR1E2,PSMC1,MCC,WDFY4,USP7,IFI35,MAP3K14,AP1M1,SLC2A5,TRAPPC10,MTA3,GOLGA3,TINAGL1,WDR8,PRG3,GAPVD1,EPB41L2,GAPT,POLR1C,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,NOV,CRISPLD2,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,UST,ZRANB1,OSBPL6,EFR3A,SRPK1,MTURN,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,PTDSS1,TXNRD2,OGDH,PAM16,TRIM26,SPPL3,BDKRB2,SNAP47,CCDC47,RARG,PEBP4,DYRK2,RNF43,DMXL1,GALNTL6,STAT4,TRAF1,F5,ST6GALNAC4,WNK1,HSD17B12,PTPRC,AP2B1,ZC3H14,SPATA5,TUBD1,RNF103-CHMP3,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,ADRBK2,ARID4A,LIMD1,CHST15,ARHGAP10,PEX2,FARP2,IDO1,NAA16,DOCK2,PIWIL2,CELF2,FYN,RBKS,ARPP19,SPOP,STK10,EPAS1,WWC2,ERMN,TMEM63A,PIK3CB,STAT3,EEFSEC,HERC1,ANKRD13A,GRK4,TMEM201,DAZAP1,PGM1,CEP128,BLVRA,SPRED2
## 1124 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,SLC29A1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,GPR176,FBXW8,MITF,SLC25A33,ABCC1,SLC7A1,SLC4A5,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,OSBPL5,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,ITGAE,SLC2A8,GATAD2A,HMBS,TTC38,NDST2,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,SLC24A3,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,TTYH3,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,SLC45A4,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,SLC39A4,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,ADORA3,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,PNPLA1,GNAO1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,P2RY2,FADD,SERPINB2,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ACSL1,ABR,DOCK1,NEMF,RAB11FIP1,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,CCL18,ELMO2,COL15A1,SLC2A9,GJB3,SGMS1,SPATS2L,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,SLC41A1,SSBP3,FOXJ3,CLRN1,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,GPR156,DENND3,FCHSD2,CDH1,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,CALML4,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,ADTRP,TMOD3,SAP30L,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,ZNF70,IL13,CCNY,DMAP1,ZNF789,SLC23A2,RREB1,PSTPIP2,TMEM154,PLA2G1B,ABCC4,ADAMTS14,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,PROZ,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,TNN,NCK2,ST3GAL4,RNF157,IKZF1,SULF2,GSTM3,TGFA,GALNT12,CEBPB,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HPD,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,SPTBN1,MYL9,GLB1,TNXB,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,SOAT2,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,COL20A1,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,SOGA1,ZNF532,EML3,ZSWIM3,SNX9,LRRN2,BCL7A,MCMBP,DNAJC3,KAT8,WNT3,GALNT7,UXS1,MTUS2,DHCR24,CDH23,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,TMEM116,ELL3,NFATC2,ZHX2,TMEM104,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,TOPBP1,PACSIN2,PIGN,CDKN2AIPNL,SERP2,WDFY2,TBC1D10A,AGAP3,MAML1,EFNB2,ATG13,CD7,LARP1,TBC1D9B,CACNA1D,STK3,KBTBD4,CHRNE,LRRC8C,P2RX7,PIK3AP1,P3H2,VPS13D,OSBPL3,ASNSD1,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,CALR3,PLLP,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,JAG1,ST7,XAF1,ERG,NEDD4L,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,IL34,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,SECISBP2L,MBD6,RCC2,PAFAH2,SLC45A3,SLIT3,USP19,IL18BP,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,NAPA,LEF1,LRRC20,RIBC2,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,DNAH1,B3GALNT2,HNMT,THADA,ELL2,RAPGEF1,AGBL4,IL16,HDAC4,EXT1,ACTN4,GPD2,C16orf45,ENO3,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,FTCDNL1,HNRNPM,SIPA1L3,RMND1,ARL6IP4,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,SRGAP3,PTPN1,UNC5B,AAK1,BEST1,CDK5RAP3,FBXL2,RAB3B,ZXDC,ABAT,ANO6,INPP5A,IKZF2,CD81,PIK3R5,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,RALY,DIDO1,ZNF175,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,ATP2C1,EHBP1,CHCHD3,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,DHX37,MVB12A,CLK3,TBC1D2,ZDHHC18,KCNAB2,ARHGAP18,EIF4G2,PELP1,CHST11,P4HTM,DGKG,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,MTA2,SIL1,LSM14A,INSC,ATP1A4,MYO9B,MYLK4,ERI3,RNF24,CD4,DNAH2,TLE4,TTC17,USPL1,ZBTB34,TMED10,LGR6,PDE9A,LAX1,AACS,MICAL1,ACAD8,MRPS27,TRPV6,PIGL,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,FNDC3B,ERAP2,ODC1,RAB20,FBXO34,YWHAQ,CSDE1,COLQ,RBM33,CRABP2,SLC36A1,RSAD2,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,PLEKHA7,MDM4,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SARNP,TESK2,ACSF2,SPNS3,SCAF11,SRC,PCBP2,SHBG,MTHFD2,TBXAS1,CRTC3,SPI1,UBE4A,LAIR1,OBSL1,SLC12A4,CCBL1,CD151,DHX15,LRRC59,EXOC3,DGAT1,LPP,ARHGAP24,ARHGEF18,NDUFV1,CD28,PPP2R5E,RFC3,NACC2,CAMP,DLGAP1,RASSF5,TMEM41A,CLTCL1,HDAC9,SLC44A4,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,KCNA2,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,FAIM2,RAD21,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,DEPDC1B,MYLK,HIPK2,SAG,SLC14A2,ILKAP,EEF2K,TRPM4,NCOA7,ASH2L,EPS15,CMTR1,ART3,WNT5B,TNFAIP8,CSGALNACT1,HMGXB4,SLMAP,PTP4A2,AGPS,FMO1,KIAA0100,ST3GAL2,BICD1,CDC42BPB,AHCYL2,CUX1,LHPP,MUC20,TMEM220,AKR1E2,PSMC1,MCC,WDFY4,USP7,RPRD1A,EFHD2,SPIDR,IFI35,MAP3K14,BANK1,WDR70,MEGF10,AP1M1,SLC2A5,TMEM51,TRAPPC10,LONRF2,MTA3,GOLGA3,TINAGL1,HNRNPLL,WDR8,CLCN1,PRG3,HECTD4,GAPVD1,EPB41L2,POLR1C,GSE1,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,NOV,CRISPLD2,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,UST,ZRANB1,OSBPL6,SRPK1,AGER,PLB1,MTURN,YEATS2,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,PTDSS1,TXNRD2,OGDH,PAM16,TRIM26,SLC22A23,SPPL3,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,REV1,PEBP4,DYRK2,RNF43,LDB2,DMXL1,GALNTL6,STAT4,TRAF1,F5,ST6GALNAC4,WNK1,BAZ1A,HSD17B12,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,SPATA5,POLR1A,TUBD1,RNF103-CHMP3,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,VANGL1,ADRBK2,CCL23,ARID4A,LIMD1,CHST15,TCF7,ARHGAP10,ECT2L,PEX2,FARP2,IDO1,NAA16,DOCK2,PIWIL2,CELF2,FYN,RBKS,ARPP19,ABTB2,MED13L,SPOP,STK10,CEBPE,EPAS1,WWC2,ERMN,ARL6IP6,TMEM63A,EIF1AD,PIK3CB,RAB19,STAT3,EEFSEC,HERC1,ANKRD13A,GRK4,SUPT3H,TIGD1,TMEM201,OR2B2,DAZAP1,PGM1,BLVRA,SPRED2
## 1125 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,FBXW8,MITF,SLC7A1,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,TRIM4,UBE2O,ARID3A,FOXJ2,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,TESC,USP32,TRPC4AP,IGF1R,TRAPPC9,UVRAG,MUC13,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,COTL1,CLIP1,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,MAP3K1,GNAO1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,P2RY2,FADD,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ABR,DOCK1,RAB11FIP1,PRKAG2,MAP1LC3B2,FHL2,DAB1,CCL18,ELMO2,SLC2A9,GJB3,SGMS1,SPATS2L,GLYR1,SLC18A2,DPPA3,SLC41A1,SSBP3,FOXJ3,CLRN1,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,DENND3,FCHSD2,CDH1,TMEM86B,FBXO7,ABCB9,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,ADTRP,TMOD3,SAP30L,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,IL13,CCNY,DMAP1,ZNF789,PSTPIP2,TMEM154,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,PROZ,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,TPCN1,MCM2,KEL,CAB39,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,TNN,NCK2,IKZF1,GSTM3,TGFA,CEBPB,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,SPTBN1,MYL9,GLB1,TNXB,DENND5A,LGALS4,HK3,SOAT2,MAN1C1,RAP1GAP2,MED12L,COL20A1,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,EML3,ZSWIM3,SNX9,LRRN2,BCL7A,MCMBP,DNAJC3,KAT8,WNT3,UXS1,MTUS2,DHCR24,CDH23,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,TTLL6,NELFCD,TESPA1,TOPBP1,PACSIN2,CDKN2AIPNL,SERP2,WDFY2,TBC1D10A,AGAP3,MAML1,EFNB2,ATG13,CD7,LARP1,TBC1D9B,CACNA1D,STK3,KBTBD4,LRRC8C,P2RX7,PIK3AP1,P3H2,VPS13D,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,CALR3,PLLP,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,JAG1,ST7,XAF1,ERG,NEDD4L,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,IL34,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,SECISBP2L,MBD6,RCC2,SLIT3,USP19,IL18BP,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,DGKI,NLRC5,RBX1,SGSM3,TGFB3,EIF6,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,NAPA,LEF1,LRRC20,RIBC2,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,ATP2A3,AHNAK,DNAH1,B3GALNT2,THADA,ELL2,RAPGEF1,AGBL4,IL16,HDAC4,EXT1,ACTN4,C16orf45,ENO3,ZNF699,GDF5,RBPMS,RASGRP1,HNRNPM,SIPA1L3,RMND1,ARL6IP4,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,SRGAP3,PTPN1,UNC5B,AAK1,BEST1,CDK5RAP3,FBXL2,RAB3B,ZXDC,ABAT,ANO6,INPP5A,IKZF2,CD81,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,RALY,ZNF175,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,EHBP1,CHCHD3,CLEC4C,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,EIF4G2,PELP1,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,MTA2,SIL1,LSM14A,INSC,ATP1A4,MYO9B,MYLK4,RNF24,CD4,DNAH2,TLE4,TTC17,USPL1,ZBTB34,TMED10,LGR6,PDE9A,LAX1,AACS,MICAL1,MRPS27,TRPV6,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,FNDC3B,ODC1,FBXO34,YWHAQ,CSDE1,COLQ,CRABP2,SLC36A1,RSAD2,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,PLEKHA7,MDM4,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,UGT1A8,UGGT1,EXD2,SMG5,SARNP,TESK2,ACSF2,SCAF11,SRC,PCBP2,SHBG,MTHFD2,CRTC3,SPI1,UBE4A,LAIR1,OBSL1,SLC12A4,CCBL1,CD151,DHX15,LRRC59,EXOC3,DGAT1,LPP,ARHGAP24,ARHGEF18,NDUFV1,CD28,PPP2R5E,RFC3,NACC2,DLGAP1,RASSF5,TMEM41A,CLTCL1,HDAC9,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,KCNA2,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,FAIM2,RAD21,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,MYLK,HIPK2,SAG,SLC14A2,ILKAP,EEF2K,TRPM4,NCOA7,ASH2L,EPS15,CMTR1,WNT5B,TNFAIP8,CSGALNACT1,HMGXB4,SLMAP,PTP4A2,AGPS,FMO1,KIAA0100,ST3GAL2,BICD1,CDC42BPB,AHCYL2,LHPP,MUC20,TMEM220,PSMC1,MCC,WDFY4,USP7,RPRD1A,EFHD2,SPIDR,IFI35,MAP3K14,BANK1,WDR70,MEGF10,AP1M1,SLC2A5,TMEM51,TRAPPC10,LONRF2,MTA3,GOLGA3,TINAGL1,HNRNPLL,WDR8,CLCN1,GAPVD1,EPB41L2,POLR1C,GSE1,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,NOV,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,ZRANB1,OSBPL6,SRPK1,AGER,MTURN,YEATS2,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,TXNRD2,OGDH,PAM16,TRIM26,SLC22A23,SPPL3,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,REV1,PEBP4,DYRK2,RNF43,LDB2,DMXL1,STAT4,TRAF1,F5,WNK1,BAZ1A,HSD17B12,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,POLR1A,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,VANGL1,ADRBK2,CCL23,LIMD1,CHST15,TCF7,ARHGAP10,ECT2L,PEX2,FARP2,NAA16,DOCK2,PIWIL2,FYN,RBKS,ARPP19,ABTB2,SPOP,STK10,CEBPE,EPAS1,WWC2,ERMN,ARL6IP6,TMEM63A,EIF1AD,PIK3CB,RAB19,STAT3,HERC1,ANKRD13A,SUPT3H,TIGD1,TMEM201,DAZAP1,PGM1,BLVRA,SPRED2
## 1126 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,TMEM229B,GUSB,TCEA2,MSMP,NHLRC4,GNB5,KCNMA1,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,LTBP2,TET3,FBP1,ELMO1,FBXW8,MITF,ABCC1,SLC7A1,TNIK,TRIM9,PRG2,C1orf105,DAPK2,TFF2,GFOD1,IL5RA,ACCS,OSBPL5,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,ZNF653,IL4,RECQL5,SEC16B,PLD3,MGLL,METRNL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,TRPC4AP,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,ITIH1,EXD3,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,SIGLEC8,ADARB1,TMEM11,KCNH2,AREL1,EPB41,EFNA3,CAPG,NGFR,ITGAE,SLC2A8,GATAD2A,HMBS,TTC38,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,PMP22,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,CHP1,VPS53,ZNF48,GUCA2A,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,KLHL6,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,DAP,TRIB1,CTIF,PC,EZH2,VPS39,ERMAP,MUSK,SUDS3,STIL,MGAT3,BSG,NT5DC3,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,CHRM1,ADGRG1,PDE6A,PDZK1,MYRIP,ITGAL,LYSMD2,VTI1A,AHDC1,MED25,TFF1,ZBTB32,NRCAM,SYNDIG1,NR2C2,CLNK,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,TRIM33,UBE3B,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,ENTPD1,SLCO3A1,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,COTL1,CLIP1,PITPNC1,DCP1B,CACUL1,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,POR,AXIN1,TTC27,MANBAL,RD3,ITPR1,CREG1,DEPDC5,ZNF428,CSNK1D,MTCL1,PILRB,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,TBC1D22A,ANKRD33B,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,KIAA1958,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,GNAO1,CACNA1S,PI4KB,SLC19A1,PCED1B,GYG1,OXNAD1,FAM151B,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,C14orf93,CMTM6,SNX29,CSRP1,GFPT2,LSM14B,DICER1,QRICH2,PLXNA2,ANKRD52,ITSN1,PNLIPRP3,FKBP1A,TRAP1,RNF144B,RPTOR,TMEM181,NCF4,P2RY2,FADD,KCNE3,DLG5,PTK2B,IL10RB,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,DPH7,SAFB2,ACSL1,ABR,DOCK1,NEMF,RAB11FIP1,PRKAG2,MAP1LC3B2,FHL2,DAB1,CCL18,ELMO2,SLC2A9,GJB3,SGMS1,SPATS2L,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,SLC41A1,SSBP3,FOXJ3,CLRN1,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,MFSD6,KCNJ15,PICALM,GNAQ,MAFK,ADAM8,FZR1,LRIG1,MED27,AQP1,DENND3,FCHSD2,CDH1,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,CALML4,PELI2,PHLDB3,UPK3A,SIAH2,MICAL2,ADTRP,TMOD3,SAP30L,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,ZNF70,IL13,CCNY,DMAP1,ZNF789,RREB1,PSTPIP2,TMEM154,PLA2G1B,ABCC4,ADAMTS14,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,PROZ,RNF214,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,LTBP4,SEMA3B,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,HECTD1,TOM1L2,NCALD,FECH,PDE6H,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,AKAP13,CHAC1,MAP3K7IP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,TNN,NCK2,RNF157,IKZF1,SULF2,GSTM3,TGFA,GALNT12,CEBPB,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,C1orf21,TRIM8,CCSER2,MIB1,C6orf106,HPD,COPS3,OSBPL1A,LRRC41,CD63,FAM53B,SPTBN1,MYL9,GLB1,TNXB,DENND5A,LGALS4,HK3,XYLT1,SOAT2,MAN1C1,METTL16,RAP1GAP2,MED12L,COL20A1,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,C16orf72,RASSF3,ZNF532,EML3,ZSWIM3,SNX9,LRRN2,BCL7A,MCMBP,DNAJC3,KAT8,WNT3,GALNT7,UXS1,MTUS2,DHCR24,CDH23,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,TOPBP1,PACSIN2,CDKN2AIPNL,SERP2,WDFY2,TBC1D10A,AGAP3,MAML1,EFNB2,ATG13,CD7,LARP1,TBC1D9B,CACNA1D,STK3,KBTBD4,LRRC8C,P2RX7,PIK3AP1,P3H2,VPS13D,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,CCDC153,DENND2D,GCM1,RNF41,COL11A2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,CALR3,PLLP,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,JAG1,ST7,XAF1,ERG,NEDD4L,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,CLDN10,VGLL4,GTSF1L,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,IL34,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,SECISBP2L,MBD6,RCC2,PAFAH2,SLIT3,USP19,IL18BP,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,GPATCH1,TMEM182,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,ARL15,WWOX,SELPLG,NAPA,LEF1,LRRC20,RIBC2,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,ZNF609,CREB3L2,ATP2A3,AHNAK,DNAH1,B3GALNT2,THADA,ELL2,RAPGEF1,AGBL4,IL16,HDAC4,EXT1,ACTN4,GPD2,C16orf45,ENO3,XPR1,ZNF699,GDF5,RBPMS,ARSG,RASGRP1,FTCDNL1,HNRNPM,SIPA1L3,RMND1,ARL6IP4,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,SRGAP3,PTPN1,UNC5B,AAK1,BEST1,CDK5RAP3,FBXL2,RAB3B,ZXDC,ABAT,ANO6,INPP5A,IKZF2,CD81,PIK3R5,TMOD1,MAP2K5,UBE2D3,SEMA3C,TRANK1,PHF12,ALDH2,RALY,DIDO1,ZNF175,SEMA4D,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,LRRC43,PLAUR,ARNT2,ATP2C1,EHBP1,CHCHD3,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,DHX37,MVB12A,CLK3,TBC1D2,KCNAB2,ARHGAP18,EIF4G2,PELP1,P4HTM,DGKG,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,MTA2,SIL1,LSM14A,INSC,ATP1A4,MYO9B,MYLK4,ERI3,RNF24,CD4,DNAH2,TLE4,TTC17,USPL1,ZBTB34,TMED10,LGR6,PDE9A,LAX1,AACS,MICAL1,ACAD8,MRPS27,TRPV6,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,FNDC3B,ERAP2,ODC1,RAB20,FBXO34,YWHAQ,CSDE1,COLQ,RBM33,CRABP2,SLC36A1,RSAD2,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,PLEKHA7,MDM4,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,UGT1A8,UGGT1,EXD2,SMG5,EARS2,SARNP,TESK2,ACSF2,SCAF11,SRC,PCBP2,SHBG,MTHFD2,TBXAS1,CRTC3,SPI1,UBE4A,LAIR1,OBSL1,SLC12A4,CCBL1,CD151,DHX15,LRRC59,EXOC3,DGAT1,LPP,ARHGAP24,ARHGEF18,NDUFV1,CD28,PPP2R5E,RFC3,NACC2,CAMP,DLGAP1,RASSF5,TMEM41A,CLTCL1,HDAC9,ACVRL1,EPHA4,GLIPR2,MCU,RALB,MLXIP,KCNA2,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,SCARA5,UPP2,IL20,ARHGEF7,SYTL3,FAIM2,RAD21,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,MYLK,HIPK2,SAG,SLC14A2,ILKAP,EEF2K,TRPM4,NCOA7,ASH2L,EPS15,CMTR1,WNT5B,TNFAIP8,CSGALNACT1,HMGXB4,SLMAP,PTP4A2,AGPS,FMO1,KIAA0100,ST3GAL2,BICD1,CDC42BPB,AHCYL2,CUX1,LHPP,MUC20,TMEM220,PSMC1,MCC,WDFY4,USP7,RPRD1A,EFHD2,SPIDR,IFI35,MAP3K14,BANK1,WDR70,MEGF10,AP1M1,SLC2A5,TMEM51,TRAPPC10,LONRF2,MTA3,GOLGA3,TINAGL1,HNRNPLL,WDR8,CLCN1,PRG3,GAPVD1,EPB41L2,POLR1C,GSE1,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,NOV,CRISPLD2,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,ZRANB1,OSBPL6,SRPK1,AGER,MTURN,YEATS2,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,RSPO4,TXNRD2,OGDH,PAM16,TRIM26,SLC22A23,SPPL3,BDKRB2,SNAP47,LRRC17,CCDC47,RARG,REV1,PEBP4,DYRK2,RNF43,LDB2,DMXL1,GALNTL6,STAT4,TRAF1,F5,WNK1,BAZ1A,HSD17B12,ZNF628,PTPRC,AP2B1,C6orf47,ZC3H14,SPATA5,POLR1A,TUBD1,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,VANGL1,ADRBK2,CCL23,ARID4A,LIMD1,CHST15,TCF7,ARHGAP10,ECT2L,PEX2,FARP2,IDO1,NAA16,DOCK2,PIWIL2,CELF2,FYN,RBKS,ARPP19,ABTB2,SPOP,STK10,CEBPE,EPAS1,WWC2,ERMN,ARL6IP6,TMEM63A,EIF1AD,PIK3CB,RAB19,STAT3,EEFSEC,HERC1,ANKRD13A,GRK4,SUPT3H,TIGD1,TMEM201,DAZAP1,PGM1,BLVRA,SPRED2
## 959 ACOT7,ZFPM1,SEC31B,ZNF862,DNAH17,EPX,LIMK2,TTC7A,MKS1,PAXBP1,ATPAF2,MSI2,LPIN1,KSR1,SNRNP200,PTAFR,ZBTB48,GUSB,TCEA2,MSMP,GNB5,TMED3,EVL,AKAP1,WDR20,MND1,TGFB1I1,PCYT1A,CABIN1,EHD1,MCEMP1,CARS2,NR0B2,BICD2,PRKCH,CD9,NISCH,ARID1A,ENG,TET3,FBP1,ELMO1,FBXW8,MITF,SLC25A33,TNIK,TRIM9,PRG2,DAPK2,OSBPL5,XXYLT1,TRIM4,UBE2O,ARID3A,FOXJ2,SLC25A26,ZNF653,RECQL5,SEC16B,PLD3,MGLL,ANAPC11,MAPK13,RAB11FIP4,LPCAT2,EPS15L1,RTN3,MIPEP,TESC,USP32,IGF1R,SLC25A25,TRAPPC9,UVRAG,MUC13,MECR,MYLK3,DOCK8,SIRT2,NARF,ACOX1,ATG14,NENF,SMURF1,RNF220,SETD1A,C19orf47,VKORC1L1,DDC,MFHAS1,PTPRS,ADARB1,TMEM11,KCNH2,AREL1,EPB41,CAPG,NGFR,SLC2A8,GATAD2A,HMBS,NDST2,PCSK6,NOLC1,ASCC1,MINK1,CLC,PNN,PIK3R6,TRERF1,RAB5C,VWCE,DIS3L2,ZNF662,UQCC1,HORMAD2,MAP3K7CL,CCM2,CBFB,EPHB2,CPSF4L,CHP1,VPS53,ZNF48,LDB3,FBXL20,CAMK2G,DENND1A,CAP1,NDFIP2,GGA2,LRRC8A,PRKCZ,ERC1,SPHK2,LDLRAD4,FADS2,TRIB1,CTIF,PC,EZH2,VPS39,MXRA7,ERMAP,SUDS3,STIL,MGAT3,BSG,PTPRE,STAR,FAXDC2,ATP11A,ANKFY1,EHF,SYT12,ACSM1,MYRIP,ITGAL,VTI1A,MED25,ZBTB32,SYNDIG1,NR2C2,CLNK,GALC,METTL17,LMAN2,ADA,CDK6,TAPBP,SAMD4B,RERE,HHAT,GALNT6,TBC1D5,CCDC174,ANGPT2,CTNNBL1,LZTFL1,RUSC2,CTSB,GRB10,MAD1L1,RB1,GALNT14,IRGC,TRIM33,HEXA,MTMR3,TFR2,RNASEH2C,SH3GL1,NCOR2,GGCX,HMGXB3,SAMD11,NDOR1,PDCL,BCKDHA,TBC1D1,RNASE7,ACP5,MTMR10,COTL1,CLIP1,LPCAT3,PITPNC1,DCP1B,RAB37,PDLIM1,LTBP1,TTC7B,PIP5K1B,INTS9,GALNT10,NVL,SLC39A4,POR,AXIN1,RD3,ITPR1,CREG1,DEPDC5,CSNK1D,MTCL1,MTFR1L,SSH1,CDCA7L,PIK3R1,SDC3,P2RX5,DAPK1,SASH1,SERPINC1,EP400,INPP4A,GEMIN4,ACTN1,THRA,ASH1L,RNF122,YPEL2,PRKCB,GALNT16,MAP3K1,PNPLA1,GNAO1,CACNA1S,PI4KB,GYG1,HK2,DYRK1A,CDYL2,MLX,BATF2,DAG1,KRT8,LGALS8,WIPI1,URI1,TLE3,UBXN11,AMPD3,SWAP70,CEL,CBFA2T2,TVP23B,BIN3,CMTM6,CSRP1,GFPT2,DICER1,QRICH2,SERINC5,ITSN1,FKBP1A,TRAP1,RNF144B,RPTOR,NCF4,FADD,SERPINB2,KCNE3,DLG5,PTK2B,NOTCH4,CAMKMT,STIM1,ITCH,MEF2D,ANXA6,SH3PXD2A,MAP4K4,SNX21,BACH1,MAP6D1,C11orf24,SAFB2,ACSL1,ABR,DOCK1,BCAS1,NEMF,RAB11FIP1,PRKAG2,MAP1LC3B2,BDH1,FHL2,CMBL,DAB1,TANGO2,ELMO2,COL15A1,GJB3,SGMS1,SPATS2L,B4GALNT3,GLYR1,MAN2A2,SLC18A2,KDM4B,DPPA3,SSBP3,FOXJ3,CLRN1,HMGCL,PHF20,SH3RF1,CYTH1,OPA1,RNF34,NRM,PDLIM7,APTX,SLC17A4,CS,KANSL1,UBAC2,NAPB,PTPRJ,CORO1C,POLM,MFSD2A,ASAP1,PICALM,GNAQ,MAFK,ADAM8,FZR1,MED27,AQP1,DENND3,FCHSD2,CDH1,TMEM86B,SPATA5L1,FBXO7,ABCB9,GRAMD1B,PELI2,UPK3A,SIAH2,MICAL2,TMOD3,SAP30L,SMARCC1,PRKCE,GPI,ARHGAP26,PAK6,ZNF70,IL13,CCNY,DMAP1,ZNF789,SLC23A2,RREB1,PSTPIP2,HCFC1R1,PLA2G1B,ABCC4,PDE4B,GNG12,IFT27,PI4KA,NADK,ZC3H11A,PROZ,USP20,TAF4B,RPS6KA2,LIN52,LRSAM1,RNF40,AK8,ZKSCAN5,RBL2,GSN,HCK,TRAF3,SEMA3B,TPCN1,MCM2,KEL,CAB39,GALM,MAP6,PPP1R1B,TOM1L2,NCALD,FECH,RNF10,FOXK1,NFIA,TTC23L,NEK3,AGPAT1,THYN1,AKAP13,CHAC1,MAP3K7IP1,SCPEP1,KIF5C,AK2,PFKFB3,RPH3A,ITPKB,VPS33A,ZDHHC3,ZNRF1,NCK2,ST3GAL4,RNF157,IKZF1,SULF2,GSTM3,TGFA,GALNT12,CEBPB,ARID1B,KMT2C,BRD4,KPNA1,CAPZB,GNG7,TRIM8,CCSER2,MIB1,C6orf106,HPD,COPS3,VOPP1,OSBPL1A,LRRC41,CD63,FAM53B,SPTBN1,MYL9,GLB1,DENND5A,ST3GAL1,LGALS4,HK3,XYLT1,SOAT2,MAN1C1,POLR3E,METTL16,RAP1GAP2,MED12L,TLDC2,COL20A1,RASSF2,BCL6B,SRPK2,APBA2,FARSA,BCAT1,COASY,PPFIA1,BOLA3,GSTO2,RASSF3,ZNF532,EML3,SNX9,MCMBP,DNAJC3,KAT8,WNT3,GALNT7,UXS1,MTUS2,DHCR24,PHF13,KLF1,ETFB,KIAA0319L,STAT1,CREBBP,WDR81,PREX1,ALOX5AP,CEP63,ANGEL1,ELL3,NFATC2,ZHX2,NXF1,SLC2A6,CACNA2D1,TTLL6,NELFCD,ABHD2,TESPA1,TOPBP1,PACSIN2,PIGN,CDKN2AIPNL,SERP2,WDFY2,TBC1D10A,AGAP3,MAML1,ATG13,PHTF2,LARP1,CACNA1D,STK3,LRRC8C,P2RX7,PIK3AP1,P3H2,OSBPL3,SEPT9,RFC2,CAPN2,HIRA,DENND2D,GCM1,RNF41,COL11A2,FAM131B,RYBP,PIP4K2A,IFI27,USP15,UCP3,TPM3,CCDC57,CALR3,STON1-GTF2A1L,PRKDC,DESI1,RFT1,GAS7,HTT,HK1,SLC7A11,MLST8,XAF1,ERG,NEDD4L,ACRBP,VAMP1,AGXT,NAP1L4,NPL,GTPBP1,CLDN10,VGLL4,MAX,CAMK1D,SLC6A4,KLHL21,NFAM1,WWP2,MAPRE3,LRRC8D,ASB8,SMYD3,RPH3AL,NUDT1,DSC1,LBR,NDRG1,ADAR,RHOBTB2,MBD6,RCC2,PAFAH2,SLIT3,USP19,SREBF2,ASIC1,LMAN2L,MYBPC3,CMIP,ITPK1,DGKI,PRICKLE2,NLRC5,RBX1,MGAT4A,SGSM3,TGFB3,EIF6,GPATCH1,RALBP1,RIC8B,ZBTB22,PHACTR1,COL4A1,WWOX,NAPA,LEF1,RIBC2,PRNP,C16orf70,ERGIC1,IQCD,DHX30,THG1L,KRT72,ZNF609,CREB3L2,NIPSNAP3B,ATP2A3,AHNAK,DNAH1,B3GALNT2,HNMT,THADA,ELL2,RAPGEF1,AGBL4,IL16,HDAC4,EXT1,ACTN4,GPD2,C16orf45,ENO3,XPR1,ZNF699,RBPMS,ARSG,RASGRP1,HNRNPM,SIPA1L3,RMND1,ARL6IP4,PTPN18,EPN2,LGR5,INPP5F,IL1B,UBR4,AFF1,WDR73,EIF3J,TFDP2,SOCS6,PVALB,IBTK,SRGAP3,PTPN1,AAK1,BEST1,CDK5RAP3,FBXL2,RAB3B,ZXDC,ABAT,ANO6,IKZF2,PIK3R5,TMOD1,MAP2K5,UBE2D3,PHF12,ALDH2,RALY,DIDO1,ZNF175,PARP9,CLSTN3,PHKB,TADA2B,TPCN2,ANKRD27,XPO7,LAMB1,PLAUR,ARNT2,ATP2C1,EHBP1,CHCHD3,ARSB,CLEC4C,FBXL13,IP6K2,GRB2,MCPH1,POC1A,MGAT4B,GPHN,AKAP12,JOSD1,PRMT3,STX3,SECISBP2,ERP29,PCCA,STT3A,DHX37,MVB12A,CLK3,TBC1D2,ZDHHC18,KCNAB2,ARHGAP18,EIF4G2,PELP1,CHST11,P4HTM,DGKG,PKD2L1,PXN,CLU,LCP1,SGPL1,MECOM,MTA2,SIL1,LSM14A,INSC,MYO9B,RNF24,CD4,DNAH2,TLE4,TTC17,USPL1,ZBTB34,TMED10,LGR6,PDE9A,LAX1,AACS,MICAL1,ACAD8,MRPS27,PIGL,GRPEL2,KCNJ6,ITPKC,RAP2A,PARVB,ERAP2,ODC1,RAB20,YWHAQ,CSDE1,CRABP2,SLC36A1,RSAD2,TKT,PTEN,SLC7A6,PRKAB1,KDELC2,ADD1,PLEKHA7,MDM4,ZBTB42,DNAJC6,ACO1,GABARAPL1,CHD9,SLC7A14,HECW2,UGT1A8,SERF2,UGGT1,EXD2,SMG5,EARS2,SARNP,TESK2,ACSF2,SCAF11,SRC,PCBP2,C20orf203,MTHFD2,TBXAS1,CRTC3,SPI1,UBE4A,LAIR1,OBSL1,SLC12A4,CCBL1,CD151,DHX15,LRRC59,EXOC3,DGAT1,LPP,ARHGAP24,ARHGEF18,NDUFV1,CD28,PPP2R5E,RFC3,NACC2,CAMP,RASSF5,CLTCL1,HDAC9,EPHA4,GLIPR2,MCU,MLXIP,NBPF20,KCNA2,CNOT8,FBXO32,IL1RL1,RAB31,STIM2,UPP2,ARHGEF7,SYTL3,FAIM2,RAD21,SPECC1L-ADORA2A,PARK7,CAMSAP1,ENTHD1,CDK17,FAM20B,DEPDC1B,MYLK,HIPK2,SAG,ILKAP,EEF2K,TRPM4,NCOA7,ASH2L,EPS15,CMTR1,WNT5B,TNFAIP8,CSGALNACT1,HMGXB4,SLMAP,PTP4A2,AGPS,FMO1,ST3GAL2,BICD1,CDC42BPB,AHCYL2,CUX1,LHPP,MUC20,TXNDC8,AKR1E2,PSMC1,MCC,WDFY4,USP7,RPRD1A,SPIDR,IFI35,MAP3K14,WDR70,AP1M1,SLC2A5,TRAPPC10,MTA3,GOLGA3,TINAGL1,HNRNPLL,WDR8,PRG3,GAPVD1,EPB41L2,GAPT,POLR1C,NR3C1,SCOC,CLASP1,HDAC1,ZEB2,RHBDD2,NOV,CRISPLD2,IQSEC1,RCAN3,SSH2,CHCHD10,GRIN3A,ABCB10,KL,UST,ZRANB1,OSBPL6,EFR3A,SRPK1,AGER,MTURN,YEATS2,KATNB1,KLHL24,TOMM34,RNF103,ARHGAP19,PTDSS1,TXNRD2,OGDH,PAM16,TRIM26,SPPL3,BDKRB2,SNAP47,CCDC47,RARG,REV1,PEBP4,DYRK2,RNF43,LDB2,DMXL1,GALNTL6,STAT4,TRAF1,F5,ST6GALNAC4,WNK1,BAZ1A,HSD17B12,ZNF628,PTPRC,AP2B1,ZC3H14,SPATA5,POLR1A,TUBD1,RNF103-CHMP3,ORAI1,ALOX15,UBASH3B,TECR,PITPNM2,NOTCH2,RANBP3,ADGRG6,ADRBK2,ARID4A,LIMD1,CHST15,TCF7,ARHGAP10,PEX2,FARP2,IDO1,NAA16,DOCK2,PIWIL2,CELF2,FYN,RBKS,ARPP19,MED13L,SPOP,STK10,CEBPE,EPAS1,WWC2,ERMN,ARL6IP6,TMEM63A,EIF1AD,PIK3CB,STAT3,EEFSEC,HERC1,ANKRD13A,GRK4,SUPT3H,TIGD1,TMEM201,DAZAP1,PGM1,CEP128,BLVRA,SPRED2## [1] 2669 8write.table(gem, file=file.path(res.dir,
paste0("gProfiler2_cra_camp_logIgE_DMPs_enrich_hypo_gwthresh_", timeStamp, ".txt")),
sep="\t", quote=F, row.names=F)
table(gem$Domain)##
## CORUM GO:BP GO:CC GO:MF HP HPA KEGG MIRNA REAC WP
## 1 956 166 149 510 375 96 308 61 47path.hypo.gw <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hypo.gw)## [1] 204 8#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hypo.gw, filter = 'top')4. enrichment gprofiler2 including CRA, CAMP and FHS
# Now including FHS but not filtering by genome-wide threshold here as we already have a smaller percentage of overlap (n=193 CpGs)
uniq.hyper <- merge_CG.all[merge_CG.all$Direction_camp_cra_fhs=="+++",]
uniq.hyper <- unique(uniq.hyper$Gene.x)
uniq.hyper <- uniq.hyper[uniq.hyper!="NA"]
uniq.hyper <- uniq.hyper[uniq.hyper!=""]
length(uniq.hyper) # 5 genes only; will end up with nothing significant so not saving them## [1] 5#[1] "CBFA2T3" "ITGA5" "B4GALT1" "FEZ2" "APBB1"
#write.table(uniq.hyper, file=file.path(res.dir,
# "cra_camp_fhs_uniq_hypermeth_genes.txt"),
# sep="\t", quote=F, row.names=F)
uniq.hypo <- merge_CG.all[merge_CG.all$Direction_camp_cra_fhs=="---",]
uniq.hypo <- unique(uniq.hypo$Gene.x)
uniq.hypo <- uniq.hypo[uniq.hypo!="NA"]
uniq.hypo <- uniq.hypo[uniq.hypo!=""]
length(uniq.hypo) # 139 genes## [1] 139write.table(uniq.hypo, file=file.path(res.dir,
paste0("cra_camp_fhs_uniq_hypometh_genes_", timeStamp, ".txt")),
sep="\t", quote=F, row.names=F)
# gprofiler2 enrichment
enrich.hyper.all <- gprofiler2::gost(query=uniq.hyper, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))## Detected custom background input, domain scope is set to 'custom'names(enrich.hyper.all)## [1] "result" "meta"gem <- enrich.hyper.all$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
# does not look very meaningful because of the gene/term size and the intersection size
head(gem); dim(gem)## GO.ID Description term_size intersection_size Domain
## 1 CORUM:2385 ITGA5-ITGB4 complex 2 1 CORUM
## 2 CORUM:2882 ITGA5-ITGB3-COL6A3 complex 3 1 CORUM
## 3 CORUM:2384 ITGA5-ITGB1-ADAM15 complex 3 1 CORUM
## 4 CORUM:143 APP-APBB1-LRP1 complex 3 1 CORUM
## 5 CORUM:3112 ITGA5-ITGB1-SPP1 complex 3 1 CORUM
## 6 CORUM:5870 APBB1-TSHZ3-HDAC1 complex 3 1 CORUM
## FDR Phenotype Genes
## 1 0.0009201427 +1 ITGA5
## 2 0.0009201427 +1 ITGA5
## 3 0.0009201427 +1 ITGA5
## 4 0.0009201427 +1 APBB1
## 5 0.0009201427 +1 ITGA5
## 6 0.0009201427 +1 APBB1## [1] 89 8write.table(gem, file=file.path(res.dir,
paste0("gProfiler2_cra_camp_fhs_logIgE_DMPs_enrich_hyper_", timeStamp, ".txt")),
sep="\t", quote=F, row.names=F)
table(gem$Domain)##
## CORUM GO:CC GO:MF KEGG REAC WP
## 10 14 20 14 20 11path.hyper.all <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hyper.all)## [1] 45 8#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hyper.all, filter = 'top')enrich.hypo.all <- gprofiler2::gost(query=uniq.hypo, organism = "hsapiens", custom_bg=uniq.ge.plt, multi_query = FALSE, evcodes=TRUE, correction_method="fdr", sources = c("GO:BP","GO:CC","GO:MF","KEGG","REAC","MIRNA", "TRANSFAC", "CORUM", "HP", "HPA", "WP"))## Detected custom background input, domain scope is set to 'custom'# for results containing all annotated terms
gem <- enrich.hypo.all$result[,c("term_id", "term_name", "term_size", "intersection_size", "source", "p_value", "intersection")]
colnames(gem) <- c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "p.Val", "Genes")
gem$FDR <- gem$p.Val
gem$Phenotype = "+1"
gem <- gem[,c("GO.ID", "Description", "term_size", "intersection_size", "Domain", "FDR", "Phenotype", "Genes")]
gem <- gem[order(gem$FDR),]
head(gem); dim(gem)## GO.ID Description term_size
## 915 MIRNA:000000 MIRNA root 14165
## 393 GO:0003674 molecular_function 17356
## 151 GO:0008150 biological_process 16625
## 152 GO:0009987 cellular process 15915
## 716 HPA:0040081 bone marrow; hematopoietic cells[≥Low] 6102
## 717 HPA:0040000 bone marrow 6102
## intersection_size Domain FDR Phenotype
## 915 110 MIRNA 9.872529e-10 +1
## 393 117 GO:MF 1.854176e-07 +1
## 151 115 GO:BP 4.535958e-07 +1
## 152 113 GO:BP 4.535958e-07 +1
## 716 63 HPA 8.133531e-07 +1
## 717 63 HPA 8.133531e-07 +1
## Genes
## 915 NDOR1,SLC2A8,NCOR2,KCNH2,NDUFS6,SAMD11,SLC19A1,ST3GAL1,SYNGAP1,RASSF2,NR0B2,LPCAT2,SIGLEC8,NHLRC4,METRNL,PCYT1A,RHOBTB2,B4GALT7,AXIN1,EZH2,ACOT7,RAB11FIP4,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,ZNF862,LRIG1,MITF,PRKCZ,TTC7A,IL13,SLC7A11,UBE2QL1,PRKCH,PAK6,ELL2,PTPRS,TNIK,MCM2,PDZD8,TRAPPC9,CAB39,MCC,AGPAT1,FBXW8,LPIN1,IL5RA,NDFIP2,DOCK1,MFHAS1,MND1,ENG,AJAP1,BICD2,DAPK2,TOMM34,SLC25A25,USP20,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,ZNF662,LMAN2,IGF1R,MECR,DAP,EPS15L1,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,LTBP4,UBE3B,TFF1,PHLDB3,LPCAT3,SLC7A1,ELMO2,RERE,PMP22,COL15A1,SSBP3,IRGC,TRERF1,ATPAF2,INPP4A,KIAA1267,SLC17A4,SLC45A4,CTSB,RCC2,LBR,NOLC1,SIK2,CLK3,GPR176,NFIA,BANK1,KSR1,TMEM86B,IL4,MICAL2,MPRIP,A2ML1
## 393 NDOR1,SLC2A8,NCOR2,KCNH2,NDUFS6,SAMD11,SLC19A1,ST3GAL1,SYNGAP1,LRRC43,RASSF2,NR0B2,LPCAT2,SIGLEC8,NHLRC4,METRNL,PCYT1A,CPSF4L,RHOBTB2,B4GALT7,AXIN1,EZH2,ACOT7,RAB11FIP4,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,ZNF862,LRIG1,MITF,PRKCZ,TTC7A,IL13,SLC7A11,UBE2QL1,PRKCH,PAK6,ELL2,PTPRS,TNIK,MCM2,PDZD8,GUCA2A,TRAPPC9,CAB39,MCC,AGPAT1,FBXW8,LPIN1,IL5RA,ACP5,NDFIP2,DOCK1,MFHAS1,MND1,PRG2,ENG,AJAP1,FBP1,BICD2,DAPK2,TOMM34,SLC25A25,USP20,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,ZNF662,LMAN2,IGF1R,MECR,DAP,EPS15L1,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,PNPLA1,LTBP4,UBE3B,TFF1,PHLDB3,LPCAT3,SLC7A1,ELMO2,RERE,PMP22,COL15A1,SSBP3,IRGC,TRERF1,ATPAF2,INPP4A,KIAA1267,SLC17A4,SLC45A4,CTSB,RCC2,LBR,NOLC1,SIK2,CLK3,GPR176,NFIA,BANK1,KSR1,TMEM86B,IL4,MICAL2,MPRIP,A2ML1
## 151 NDOR1,SLC2A8,NCOR2,KCNH2,NDUFS6,SAMD11,SLC19A1,ST3GAL1,SYNGAP1,RASSF2,NR0B2,LPCAT2,SIGLEC8,NHLRC4,METRNL,PCYT1A,CPSF4L,RHOBTB2,B4GALT7,AXIN1,EZH2,ACOT7,RAB11FIP4,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,ZNF862,LRIG1,MITF,PRKCZ,TTC7A,IL13,SLC7A11,UBE2QL1,PRKCH,PAK6,ELL2,PTPRS,TNIK,MCM2,PDZD8,GUCA2A,TRAPPC9,CAB39,MCC,AGPAT1,FBXW8,LPIN1,IL5RA,ACP5,NDFIP2,DOCK1,MFHAS1,MND1,PRG2,ENG,AJAP1,FBP1,BICD2,DAPK2,TOMM34,SLC25A25,USP20,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,ZNF662,LMAN2,IGF1R,MECR,DAP,EPS15L1,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,PNPLA1,LTBP4,UBE3B,TFF1,LPCAT3,SLC7A1,ELMO2,RERE,PMP22,COL15A1,SSBP3,IRGC,TRERF1,ATPAF2,INPP4A,KIAA1267,SLC17A4,SLC45A4,CTSB,RCC2,LBR,NOLC1,SIK2,CLK3,GPR176,NFIA,BANK1,KSR1,TMEM86B,IL4,MICAL2,MPRIP,A2ML1
## 152 NDOR1,SLC2A8,NCOR2,KCNH2,NDUFS6,SAMD11,SLC19A1,ST3GAL1,SYNGAP1,RASSF2,NR0B2,LPCAT2,SIGLEC8,NHLRC4,METRNL,PCYT1A,CPSF4L,RHOBTB2,B4GALT7,AXIN1,EZH2,ACOT7,RAB11FIP4,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,ZNF862,MITF,PRKCZ,TTC7A,IL13,SLC7A11,UBE2QL1,PRKCH,PAK6,ELL2,PTPRS,TNIK,MCM2,PDZD8,GUCA2A,TRAPPC9,CAB39,MCC,AGPAT1,FBXW8,LPIN1,IL5RA,ACP5,NDFIP2,DOCK1,MFHAS1,MND1,PRG2,ENG,AJAP1,FBP1,BICD2,DAPK2,TOMM34,SLC25A25,USP20,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,ZNF662,LMAN2,IGF1R,MECR,DAP,EPS15L1,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,PNPLA1,LTBP4,UBE3B,TFF1,LPCAT3,SLC7A1,ELMO2,RERE,PMP22,COL15A1,SSBP3,IRGC,TRERF1,ATPAF2,INPP4A,KIAA1267,SLC17A4,CTSB,RCC2,LBR,NOLC1,SIK2,CLK3,GPR176,NFIA,BANK1,KSR1,TMEM86B,IL4,MICAL2,MPRIP,A2ML1
## 716 NDOR1,NCOR2,NDUFS6,ST3GAL1,LPCAT2,PCYT1A,B4GALT7,AXIN1,EZH2,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,LRIG1,MITF,PRKCZ,TTC7A,PRKCH,TNIK,MCM2,CAB39,AGPAT1,FBXW8,LPIN1,DOCK1,MND1,PRG2,BICD2,TOMM34,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,LMAN2,IGF1R,MECR,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,LTBP4,UBE3B,PHLDB3,SLC7A1,ELMO2,COL15A1,TRERF1,ATPAF2,INPP4A,KIAA1267,CTSB,RCC2,LBR,CLK3,GPR176,NFIA,BANK1,MICAL2,MPRIP
## 717 NDOR1,NCOR2,NDUFS6,ST3GAL1,LPCAT2,PCYT1A,B4GALT7,AXIN1,EZH2,CREBBP,SLC25A26,GUSB,SPI1,ZFPM1,LRIG1,MITF,PRKCZ,TTC7A,PRKCH,TNIK,MCM2,CAB39,AGPAT1,FBXW8,LPIN1,DOCK1,MND1,PRG2,BICD2,TOMM34,LRSAM1,EVL,MSI2,TOLLIP,HDAC1,LMAN2,IGF1R,MECR,EZR,EPX,SEC16B,AQP1,ARID3A,MAD1L1,LTBP4,UBE3B,PHLDB3,SLC7A1,ELMO2,COL15A1,TRERF1,ATPAF2,INPP4A,KIAA1267,CTSB,RCC2,LBR,CLK3,GPR176,NFIA,BANK1,MICAL2,MPRIP## [1] 953 8write.table(gem, file=file.path(res.dir,
paste0("gProfiler2_cra_camp_fhs_logIgE_DMPs_enrich_hypo_", timeStamp, ".txt")),
sep="\t", quote=F, row.names=F)
table(gem$Domain)##
## CORUM GO:BP GO:CC GO:MF HP HPA KEGG MIRNA REAC WP
## 150 228 14 66 257 195 4 22 14 3path.hypo.all <- gem[gem$Domain=="KEGG" | gem$Domain=="REAC" | gem$Domain=="WP",]
dim(path.hypo.all)## [1] 21 8#highlights terms with only kegg/Reactome or Wiki pathways
DT::datatable(path.hypo.all, filter = 'top')5. clusterProfileR enrichment analysis for CRA and CAMP
bck.univ.plt <- mapIds(org.Hs.eg.db, uniq.ge.plt, 'ENTREZID', 'SYMBOL')## 'select()' returned 1:many mapping between keys and columnslength(unique(bck.univ.plt))## [1] 22656bck.univ.plt.df <- data.frame(bck.univ.plt)
#bck.univ.plt.df <- bck.univ.plt.df[!is.na(bck.univ.plt.df$bck.univ.plt), ]
bck.univ.plt.df <- bck.univ.plt.df$bck.univ.plt
univ <- as.numeric(bck.univ.plt.df)
univ <- univ[!is.na(univ)]
univ <- as.character(univ)
#ids <- as.numeric(symbols.entrez)
#names(geneList) <- ids
coeff.cra <- merge_CG_gw$beta_coeff_cra
names(coeff.cra) <- merge_CG_gw$Gene.x
coeff.cra.df <- data.frame(coeff.cra)
coeff.cra.df$Gene <- names(coeff.cra)
coeff.cra.uniq <- coeff.cra.df$Gene[!is.na(coeff.cra.df$Gene)]
coeff.cra.uniq <- coeff.cra.df[!is.na(coeff.cra.df$Gene), ]
coeff.cra.uniq <- coeff.cra.df[coeff.cra.df$Gene!="NA",]
coeff.cra.uniq <- coeff.cra.df[!duplicated(coeff.cra.df$Gene), ]
coeff.cra.uniq.v <- coeff.cra.uniq$coeff.cra
names(coeff.cra.uniq.v) <- coeff.cra.uniq$Gene
geneList <- coeff.cra.uniq.v
geneList <- sort(geneList, decreasing = TRUE)
entrezid <- names(geneList)
symbols.entrez <- mapIds(org.Hs.eg.db, entrezid, 'ENTREZID', 'SYMBOL')## 'select()' returned 1:1 mapping between keys and columnslength(symbols.entrez)## [1] 1509#ids <- as.numeric(symbols.entrez)
length(unique(symbols.entrez))## [1] 1390ids <- lapply(symbols.entrez, as.numeric)
#ids <- as.numeric(symbols.entrez)
names(geneList) <- ids
gene <- names(geneList)
edo.dgn <- enrichDGN(gene, pvalueCutoff = 0.05,pAdjustMethod = "BH",qvalueCutoff = 0.05)
barplot(edo.dgn, showCategory=20)
edo.dgn.ge <- setReadable(edo.dgn, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(edo.dgn.ge, categorySize="qvalue", foldChange=geneList)## Warning: ggrepel: 96 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
# without fold change
cnetplot(edo.dgn.ge, node_label="all", categorySize="qvalue")## Warning: ggrepel: 77 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
enrichplot::dotplot(edo.dgn.ge, showCategory=30) + ggtitle("dotplot for DO")## wrong orderBy parameter; set to default `orderBy = "x"`
pdf(file = file.path(sub.plots.dir, "dotplot_enrichDGN_CRA_CAMP.pdf"),width = 7, height = 7)
enrichplot::dotplot(edo.dgn.ge, showCategory=20) + ggtitle("dotplot for DO")## wrong orderBy parameter; set to default `orderBy = "x"`dev.off()## png
## 2DT::datatable(edo.dgn.ge@result, filter = 'top')## Warning in instance$preRenderHook(instance): It seems your data is too big
## for client-side DataTables. You may consider server-side processing: https://
## rstudio.github.io/DT/server.html# no gene sets enriched here for diseases using DysGeNET
gse.dgn <- gseDGN(geneList,
minGSSize = 10,
maxGSSize = 500,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
verbose = TRUE)## preparing geneSet collections...## GSEA analysis...## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize,
## gseaParam, : There are duplicate gene names, fgsea may produce unexpected
## results.## no term enriched under specific pvalueCutoff...#dgn <- setReadable(dgn, 'org.Hs.eg.db')
#head(dgn, 3)
#enrichplot::dotplot(gse.dgn, showCategory=30) + ggtitle("dotplot for DO")
# Enrichment map organizes enriched terms into a network with edges connecting overlapping gene sets. In this way, mutually overlapping gene sets are tend to cluster together, making it easy to identify functional module
x <- pairwise_termsim(edo.dgn.ge)
emapplot(x)
pdf(file = file.path(sub.plots.dir, "enrichmentMap_pairwise_gseDGN_CRA_CAMP_overlap_gw_genes.pdf"),
width = 11, height = 9)
emapplot(x)
dev.off()## png
## 2# nothing
enr.do <- enrichDO(gene = gene,
ont = "DO",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe = univ,
minGSSize = 10,
maxGSSize = 500,
qvalueCutoff = 0.05,
readable = FALSE)
dim(enr.do) # nothing## [1] 0 9head(enr.do)## [1] ID Description GeneRatio BgRatio pvalue p.adjust
## [7] qvalue geneID Count
## <0 rows> (or 0-length row.names)gene.df <- bitr(gene, fromType = "ENTREZID",
toType = c("ENSEMBL", "SYMBOL"),
OrgDb = org.Hs.eg.db)## 'select()' returned 1:many mapping between keys and columns## Warning in bitr(gene, fromType = "ENTREZID", toType = c("ENSEMBL", "SYMBOL"), :
## 1.37% of input gene IDs are fail to map...head(gene.df)## ENTREZID ENSEMBL SYMBOL
## 1 3508 ENSG00000132740 IGHMBP2
## 2 4507 ENSG00000099810 MTAP
## 3 57705 ENSG00000128815 WDFY4
## 4 83445 ENSG00000111305 GSG1
## 6 90957 ENSG00000163214 DHX57
## 7 23136 ENSG00000082397 EPB41L3# just returns functional profile of a geneset at a specific GO level not a P-value
ggo <- groupGO(gene = gene,
OrgDb = org.Hs.eg.db,
ont = "BP",
level = 2,
readable = TRUE)
dim(ggo)## [1] 31 5head(ggo)## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 92 92/1390
## GO:0002376 GO:0002376 immune system process 295 295/1390
## GO:0006791 GO:0006791 sulfur utilization 0 0/1390
## GO:0006794 GO:0006794 phosphorus utilization 0 0/1390
## GO:0007610 GO:0007610 behavior 45 45/1390
## GO:0008152 GO:0008152 metabolic process 892 892/1390
## geneID
## GO:0000003 ZMIZ1/TGFBR2/ROPN1L/ADAM19/ZNF148/TRIM27/ASB1/CYP19A1/VDR/OPRM1/APP/ETV6/CREB3L4/PARK7/STAT3/DHX37/ELL3/RAD21/THRA/STAR/STK3/PTEN/IL1B/IFT27/EPAS1/TESK2/SLC6A4/DNAH1/SGPL1/DHCR24/SRPK1/GOLGA3/CALR3/LGR5/ACOX1/NCOR2/FBXW8/DAZAP1/ABHD2/RARG/NR2C2/SLIT3/ADA/SPATA5/PPP1R1B/ASH1L/PLB1/TAF4B/TCF7/SMARCC1/PIWIL2/SRC/TXNDC8/TGFB3/POC1A/IDO1/CAPN2/CD9/ARID4A/ACRBP/KLF1/GJB3/KRT8/SLC2A8/CEBPB/NUDT1/SLC19A1/WNT3/SIRT2/ADGRG1/BSG/CSDE1/ANGPT2/SAFB2/ABAT/FZR1/SPHK2/NOTCH2/GRB2/ARID1A/ATP1A4/HDAC4/HORMAD2/PTK2B/LIMK2/QRICH2/PTAFR/MND1/LEF1/CTSB/GCM1/PRKDC
## GO:0002376 ABL1/ZMIZ1/TGFBR2/GM2A/DEFA4/VAV2/SLPI/TARM1/MARCO/CLEC5A/TRIM27/MPO/SLC7A7/GDI2/CYP19A1/SIRPA/UBASH3B/AZU1/AP1G1/OPRM1/TNFRSF1B/DYNC1H1/TNF/KIF13B/APP/NLRC4/ABCA13/ETV6/MIR145/CCRL2/HLX/GPR68/MYO18A/PSMB7/LRRK1/TREM2/FCN1/JARID2/IL18RAP/LTF/IL20/SIPA1L3/PARK7/STAT1/DOCK2/IL16/SRPK2/STAT3/IL10RB/PRG3/IFI35/HK1/SERPINC1/THRA/STAR/GAPT/DNAJC3/STK3/TRAF3/IL1B/RNF41/ITCH/BANK1/MECOM/PSMA2/EPAS1/MFSD6/SLC7A11/NOTCH4/EIF6/SH3RF1/TRIM8/ASH2L/SWAP70/HDAC9/KMT2C/PDE4B/SGPL1/CAPZB/RAB3B/LRRC8A/ATP11A/SRPK1/IL34/RASSF2/AMPD3/LAIR1/TMOD3/GLB1/SOCS6/RAB31/TAPBP/AGBL4/CCL23/NLRC5/GSN/CD4/IP6K2/FARP2/GPI/GTPBP1/ANO6/CREG1/CAMK1D/RARG/RNASE7/TRIB1/ADD1/ADAR/PTPN1/P4HTM/FKBP1A/PRKCB/IL1RL1/LRRC17/AGER/ADA/PIP4K2A/LSM14A/ZNF175/CD63/DLG5/CD81/PIK3R6/ERAP2/PRNP/PLAUR/CAB39/ORAI1/ALOX15/CD151/HDAC1/CLU/JAG1/TCF7/MSMP/ADAM8/NFAM1/XAF1/STK10/ADTRP/IFI27/CAP1/NCK2/CBFB/SSBP3/WNK1/SPI1/PILRB/ADARB1/SRC/IL13/LCP1/NDRG1/TGFB3/IDO1/CD9/ARID4A/SELPLG/PIK3CB/IL18BP/SETD1A/RSAD2/PRKCE/PREX1/KLF1/MTURN/NCF4/TMEM63A/PSMC1/RAPGEF1/CDK6/RAB20/CEBPE/UBR4/ABCB9/CREBBP/DOCK1/CD28/CRISPLD2/MYL9/CEBPB/CLEC4C/FAXDC2/SDC3/SLC2A5/LAX1/AP1M1/CLC/CALM1/HK3/HCK/GYG1/CAMK2G/PLA2G1B/MITF/SLC7A6/SH3PXD2A/CTNNBL1/SIRT2/FOXP1/ACTN1/IL4/CRTC3/SERINC5/RB1/MUC13/SEMA3C/BSG/LBR/TRPM4/ABR/KAT8/BATF2/AP2B1/CD59/PARP9/P2RX7/DSC1/CAMP/CDK5RAP3/KCNAB2/ELMO2/DGAT1/FADD/ANGPT2/OSBPL1A/CD7/USP15/PIK3R1/ITPKB/MCEMP1/PLD3/KLHL6/FBXO7/TESC/NFATC2/PICALM/ELMO1/SPPL3/EPX/TESPA1/SLC7A1/CCL18/PRKCZ/SPHK2/IL5RA/NOTCH2/BCL6B/PTPRC/PRG2/GRB2/MCU/SEMA4D/CLNK/MUC20/ITGAL/POLR3E/IGF1R/HDAC4/PTK2B/ARSB/COTL1/MFHAS1/TRIM26/PCBP2/PTPRJ/TTC7A/VPS33A/POLM/RAB5C/DAPK1/PTAFR/DOCK8/GUSB/IKZF1/FYN/CMTM6/LEF1/EFNB2/EVL/ERMAP/HIPK2/RASGRP1/PGM1/PRKCH/MAP3K1/CTSB/RAB37/TRIM4/PRKDC/DAPK2/MAP3K14/MAD1L1/ZFPM1
## GO:0006791
## GO:0006794
## GO:0007610 GM2A/NGF/OPRM1/APP/PARK7/MFSD2A/STAT3/THRA/STAR/KCNA2/PTEN/EPHB2/SLC7A11/SLC6A4/INPP5F/PAK6/FBXL20/EPHA4/ASIC1/AGER/ADA/PPP1R1B/PRNP/DAB1/ADARB1/APBA2/IDO1/CAPN2/PRKCE/CEBPB/CDH23/TMOD1/FADD/MUSK/DGKI/HTT/PICALM/ABAT/PRKCZ/GNAO1/HDAC4/SLC18A2/FYN/HIPK2/GPR176
## GO:0008152 IGHMBP2/MTAP/WDFY4/ABL1/NEDD9/ZMIZ1/TGFBR2/XYLT1/GM2A/RBKS/CUX1/PCOLCE2/KIDINS220/VAV2/TERF2/SLPI/ROPN1L/ADAM19/CAMKK2/SMYD4/NAV3/LIPC/MARCO/TPP1/CLEC5A/ZNF148/TRIM27/ADGB/NGF/MIF4GD/MPO/PPM1H/MGAT5/UCK2/TUT1/SLC7A7/ASB1/GLIPR2/ADCY9/SSH2/ZDHHC14/SYNJ2/CYP19A1/TGOLN2/SIRPA/TFR2/FKBP9/ATN1/ACOXL/RHBDF2/ME3/CELF2/TMEM150B/UBASH3B/VDR/HIPK3/AZU1/ACACA/OPRM1/TNFRSF1B/DYNC1H1/TNF/MKNK1/TGFBI/POLE/PIK3C2B/RBM20/MACROD1/TRIM67/APP/NLRC4/CHST11/ZNF438/MOK/PPP2R5C/ETV6/MIR145/RUFY4/GPX3/HLX/LITAF/FKBP15/EFR3B/PRDX5/MYO18A/INTS6/PSMB7/LRRFIP1/KLHL25/IRAK2/LRRK1/CYB561D1/CRYL1/PCK2/TREM2/FCN1/JARID2/IL18RAP/PCGF3/LTF/CPM/ARRDC5/CREB3L4/FAM168A/SUFU/HSD17B12/FBXL2/ZBTB34/RALB/SECISBP2/F5/TECR/ZC3H14/ANKRD13A/RNF157/AKR1E2/ATP2A3/ART3/IL20/ERP29/ODC1/HECTD4/ITPKC/PARK7/STAT1/EXT1/MFSD2A/EEFSEC/IL16/COL15A1/ZNF699/SRPK2/STAT3/USP7/ACAD8/PITPNM2/DHX37/ELL2/RFT1/WIPI1/CCM2/STT3A/RALY/UCP3/MYLK4/ZKSCAN5/ACO1/WWOX/UBXN11/RNF10/PHACTR1/PRG3/CHCHD3/ZNRF1/FARSA/SPIDR/ELL3/RAD21/HK1/HECTD1/BAZ1A/KL/SERPINC1/SMYD3/BACH1/THRA/YEATS2/ATG13/DPPA3/MGAT4B/THG1L/STAR/KEL/P3H2/TOPBP1/DNAJC3/HIRA/ERI3/PDE9A/SLC2A9/BICD1/STK3/MIB1/TRAF3/PTEN/IL1B/TNXB/GSTO2/CBFA2T2/ARL6IP4/RNF41/ITCH/HNRNPM/BANK1/AGAP3/BRD4/ZDHHC3/EPHB2/MECOM/PSMA2/GLYR1/CDC42BPB/SAMD4B/NT5DC3/VPS39/ZNF609/LARP1/FOXJ3/VGLL4/CAMKMT/PPP2R5E/LHPP/WDFY2/EPAS1/TESK2/KLHL24/MTHFD2/ST3GAL2/PI4KA/AHCYL2/BLVRA/AK2/ZNF789/METTL17/SLC7A11/NOTCH4/CREB3L2/EIF6/LSM14B/SH3RF1/TRIM8/FBXL13/SLC6A4/BCKDHA/ASH2L/ANGEL1/TGFA/OBSL1/AACS/SWAP70/HDAC9/AKAP12/ZC3H11A/KMT2C/PDE4B/WWC2/GALM/CRABP2/TRERF1/HMGCL/CSNK1D/HPD/ACSM1/HERC1/GEMIN4/ZDHHC18/SUDS3/UBE2D3/SGPL1/OGDH/RMND1/GDF5/REV1/RNF103/PIP5K1B/POR/NR3C1/NXF1/SCPEP1/RAB3B/WDR70/CHAC1/DHCR24/EARS2/SLC45A3/OPA1/INPP5F/GALNT16/SREBF2/ZXDC/SRPK1/IL34/AGPS/RASSF2/AMPD3/LGALS8/DESI1/MED12L/GLB1/NEK3/ZBTB42/GNAQ/PELP1/SOCS6/RAB31/TAPBP/TCEA2/BCAT1/ACOX1/FOXK1/AGBL4/ALOX5AP/MAFK/RPTOR/CCL23/NLRC5/PAM16/NCOR2/AGPAT1/GSN/CD4/SIAH2/IP6K2/PHF20/EXD2/PAK6/MICAL1/TRAF1/GPI/FBXL20/GTPBP1/RHBDD2/FBXW8/DAZAP1/MTA3/FECH/ABHD2/CREG1/APTX/CAMK1D/MTFR1L/RARG/BDKRB2/EFNA3/SAP30L/PHF12/RNASE7/ACSF2/TRIB1/PNN/CS/ADD1/ADAR/EPS15/MAP6D1/PTPN1/TXNRD2/NPL/P4HTM/ASB8/AAK1/NR2C2/GALC/FKBP1A/SERPINB2/PRKCB/CHST15/USP32/EPHA4/URI1/ZNF628/UST/NELFCD/NDST2/NACC2/IL1RL1/PDE6H/DHX15/CORO1C/AGER/UGT1A8/SLIT3/ADA/PIP4K2A/LSM14A/MICAL2/ZNF175/DEPDC5/PPP1R1B/CD63/EHF/ASH1L/NVL/SAG/SECISBP2L/RPRD1A/PLB1/VTI1A/EP400/KANSL1/MCPH1/POLR1C/CTIF/RNASEH2C/FBXO32/ERC1/SERP2/CD81/PIGN/SARNP/RBL2/PIK3R6/ERAP2/PRNP/SULF2/ITSN1/PELI2/PLAUR/TTLL6/HNRNPLL/TFF1/GGCX/DIDO1/IFRD1/CAB39/ALOX15/ARNT2/ENO3/TAF4B/HDAC1/CLU/AGXT/MED13L/JAG1/TCF7/GALNT7/ZHX2/ERG/MED25/PI4KB/UBAC2/ACTN4/DYRK1A/MAP2K5/ADAM8/RYBP/NENF/CSGALNACT1/NFAM1/HMBS/ZEB2/HEXA/SCOC/NOLC1/INPP5A/SPOP/BCL7A/STK10/ADTRP/TMEM86B/DAB1/CHP1/DENND3/RNF220/GPD2/COPS3/MTCL1/IFI27/LDLRAD4/NCK2/CBFB/SSBP3/CMBL/TPCN2/ATG14/TRPC4AP/COASY/WNK1/SMARCC1/MVB12A/DCP1B/SPI1/SLC24A3/USP19/PIWIL2/YWHAQ/GALNTL6/PEX2/PILRB/ADAMTS14/GSTM3/MAN1C1/DNAJC6/ADARB1/SRC/IL13/CLK3/TXNDC8/PHKB/TGFB3/APBA2/LAMB1/ST6GALNAC4/JOSD1/PCSK6/ADORA3/MAPRE3/MCM2/MTMR10/IBTK/SSH1/TFDP2/SLC2A6/MAPK13/ACSL1/IDO1/MDM4/LTBP4/CHCHD10/PC/SLC17A4/CAPN2/CD9/ST3GAL1/ARSG/ARID4A/PIK3CB/SETD1A/RSAD2/PRKCE/SLC29A1/PCCA/PREX1/MLX/RNF24/PIGL/KLF1/RNF34/PFKFB3/MTURN/TET3/TPCN1/ZNF70/NCF4/SMURF1/MAML1/MRPS27/UVRAG/MAP4K4/PSMC1/RAPGEF1/ANAPC11/UGGT1/CDK6/AHNAK/MLST8/RBPMS/MTA2/ABCC1/PTPRE/DIS3L2/CEBPE/VPS13D/UXS1/UBR4/ZRANB1/CREBBP/NEMF/DAG1/ZNF662/PTDSS1/KLHL21/CD28/ARID3A/GPATCH1/KDM4B/CHD9/TADA2B/METTL16/ARPP19/PRKAB1/FOXJ2/RASSF5/RAB19/SLCO3A1/SLC2A8/ETFB/USP20/MIR1207/CEBPB/LRRC41/LIN52/XXYLT1/MYLK/FAXDC2/SDC3/CEL/SLC2A5/TNIK/FMO1/ARID1B/NUDT1/TRIM9/LAX1/ITPK1/RD3/FAM20B/NISCH/CLC/AKAP13/SLC19A1/LDB2/CDYL2/STAT4/CALM1/NEDD4L/HK3/GFPT2/RFC3/MBD6/SMG5/TLE4/HCK/NAA16/GYG1/CMTR1/RAP2A/CAMK2G/FHL2/ACVRL1/PLA2G1B/MGAT3/RNF144B/PRKAG2/GATAD2A/MITF/INTS9/SH3PXD2A/WNT3/EXD3/CTNNBL1/SGSM3/SIRT2/DAP/MCMBP/WWP2/CNOT8/LIMD1/FOXP1/RNF122/RPS6KA2/DYRK2/NADK/RNF40/ACTN1/IL4/CRTC3/SERINC5/RB1/ACCS/MUC13/UQCC1/ADGRG1/PAFAH2/BSG/RNF214/GALNT6/CSDE1/SUPT3H/LBR/MAX/NFIA/TRPM4/KAT8/BATF2/MECR/MINK1/MAP1LC3B2/SOAT2/GALNT10/AP2B1/MED27/PARP9/HNMT/P2RX7/TTC7B/NDUFV1/CDK5RAP3/KCNAB2/DPH7/UPP2/POLR1A/ITIH1/SLC7A14/DGAT1/FADD/MUSK/THADA/ANGPT2/WDR81/TKT/OSBPL1A/RBX1/TBXAS1/PNPLA1/DGKI/MEF2D/FADS2/HTT/ZBTB32/USP15/AK8/PIK3R1/NDOR1/MIR548AZ/ITPKB/DGKG/PDLIM1/CCDC47/TLE3/TRAP1/SAFB2/NCOA7/PLD3/KPNA1/EFR3A/TBC1D5/SEC16B/ZBTB22/CPSF4L/PRMT3/SASH1/FBXO7/GALNT12/COLQ/TESC/NFATC2/AFF1/PICALM/GRB10/CCNY/TGFB1I1/SPPL3/SGMS1/OSBPL3/EPX/GGA2/PIK3R5/RERE/ABCC4/ABAT/ENTPD1/CCL18/DMAP1/RECQL5/PTPN18/SLC25A33/FZR1/PRKCZ/SPHK2/NGFR/PTPRS/MLXIP/IL5RA/ALDH2/GALNT14/PNLIPRP3/NOTCH2/AXIN1/RFC2/ASCC1/BCL6B/UBE2O/SPTBN1/MAN2A2/PTPRC/RREB1/TMED10/GRB2/PXN/NR0B2/TRIM33/SNRNP200/ST3GAL4/SPRED2/TBC1D10A/SLC44A4/VKORC1L1/SEMA4D/ILKAP/CDCA7L/ASNSD1/CLNK/ARID1A/CARS2/MUC20/PAXBP1/DDC/EIF1AD/PCYT1A/POLR3E/IGF1R/HDAC4/BDH1/WDR20/MGLL/EIF4G2/LPIN1/IKZF2/AQP1/PTK2B/ARSB/DICER1/RNF43/GUCA2A/RCAN3/GRK4/MFHAS1/UBE4A/TRIM26/LIMK2/HHAT/INPP4A/PCBP2/EEF2K/UBE3B/PTPRJ/SLC18A2/TTC7A/QRICH2/ZNF48/GPHN/PROZ/VPS33A/GFOD1/NDFIP2/LTBP1/MTMR3/SLC25A25/FBP1/POLM/ZNF653/DAPK1/LPCAT3/OXNAD1/PTAFR/B3GALNT2/MGAT4A/GUSB/LRSAM1/IKZF1/FYN/MND1/SOGA1/SCAF11/SLC4A5/TRAPPC9/PTP4A2/HECW2/MYLK3/AREL1/ENG/LPCAT2/CDH1/OSBPL6/LEF1/ITPR1/EFNB2/USPL1/ACP5/ERMAP/HIPK2/RASGRP1/PGM1/PRKCH/TNFAIP8/MAP3K1/CTSB/MIPEP/HK2/EZH2/TRIM4/CACUL1/SAMD11/GCM1/CABIN1/GABARAPL1/ZBTB48/CDK17/PRKDC/NHLRC4/EIF3J/OSBPL5/MIR202/SNX9/DAPK2/SLC23A2/MAP3K14/KSR1/ZNF862/ACOT7/ZFPM1ego <- enrichGO(gene = gene,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
readable = TRUE)
dim(ego) # 251## [1] 251 9save(ego, file=file.path(res.dir,
paste0("enrich_GO_CRA_CAMP_gwthreshV1_", timeStamp, ".RData")))
write.table(ego@result,file=file.path(res.dir,
paste0("enrichGO_CRA_CAMP_gwthreshV1_",timeStamp,".txt"))
,sep="\t",row.names=F,quote=F)
head(ego)## ID Description
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:0045637 GO:0045637 regulation of myeloid cell differentiation
## GO:1903706 GO:1903706 regulation of hemopoiesis
## GO:1902105 GO:1902105 regulation of leukocyte differentiation
## GO:0043312 GO:0043312 neutrophil degranulation
## GO:0002283 GO:0002283 neutrophil activation involved in immune response
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0030099 71/1233 431/18866 4.110661e-13 2.338144e-09 1.981339e-09
## GO:0045637 45/1233 263/18866 2.506735e-09 7.129156e-06 6.041233e-06
## GO:1903706 68/1233 498/18866 5.649299e-09 9.610415e-06 8.143847e-06
## GO:1902105 47/1233 290/18866 6.758379e-09 9.610415e-06 8.143847e-06
## GO:0043312 64/1233 487/18866 6.862848e-08 7.807176e-05 6.615786e-05
## GO:0002283 64/1233 490/18866 8.630413e-08 8.181632e-05 6.933099e-05
## geneID
## GO:0030099 TGFBR2/CLEC5A/UBASH3B/TNF/APP/MIR145/GPR68/LRRK1/TREM2/LTF/IL20/STAT1/STAT3/THRA/RNF41/EPAS1/EIF6/ASH2L/KMT2C/IL34/RASSF2/TMOD3/CD4/FARP2/RARG/TRIB1/ADD1/ADAR/P4HTM/PRKCB/LRRC17/PIP4K2A/CD81/HDAC1/JAG1/CBFB/SPI1/SRC/ARID4A/SETD1A/KLF1/MTURN/CDK6/CEBPE/CREBBP/MYL9/CEBPB/FAXDC2/MITF/SH3PXD2A/FOXP1/ACTN1/IL4/RB1/LBR/KAT8/BATF2/CDK5RAP3/FADD/PIK3R1/ITPKB/TESC/NOTCH2/PTK2B/MFHAS1/VPS33A/IKZF1/LEF1/HIPK2/PRKDC/ZFPM1
## GO:0045637 UBASH3B/TNF/MIR145/GPR68/TREM2/LTF/IL20/STAT1/STAT3/RNF41/EIF6/ASH2L/KMT2C/IL34/RASSF2/CD4/RARG/TRIB1/P4HTM/PRKCB/LRRC17/HDAC1/JAG1/CBFB/SPI1/SETD1A/MTURN/CDK6/CREBBP/MYL9/CEBPB/FAXDC2/MITF/FOXP1/IL4/RB1/FADD/PIK3R1/ITPKB/TESC/NOTCH2/PTK2B/LEF1/PRKDC/ZFPM1
## GO:1903706 ABL1/ZMIZ1/TGFBR2/UBASH3B/TNF/MIR145/HLX/GPR68/PSMB7/TREM2/LTF/IL20/STAT1/STAT3/IL1B/RNF41/ITCH/PSMA2/EIF6/SH3RF1/ASH2L/KMT2C/IL34/RASSF2/CD4/RARG/TRIB1/P4HTM/PRKCB/LRRC17/AGER/ADA/PIK3R6/HDAC1/JAG1/TCF7/ADAM8/NFAM1/CBFB/SPI1/SETD1A/MTURN/PSMC1/CDK6/CREBBP/CD28/MYL9/CEBPB/FAXDC2/MITF/FOXP1/IL4/RB1/FADD/PIK3R1/ITPKB/FBXO7/TESC/NFATC2/TESPA1/PRKCZ/NOTCH2/PTPRC/PTK2B/LEF1/RASGRP1/PRKDC/ZFPM1
## GO:1902105 ABL1/ZMIZ1/TGFBR2/UBASH3B/TNF/MIR145/HLX/GPR68/TREM2/LTF/IL20/IL1B/RNF41/SH3RF1/IL34/RASSF2/CD4/TRIB1/LRRC17/AGER/ADA/PIK3R6/TCF7/ADAM8/NFAM1/CBFB/CDK6/CD28/CEBPB/MITF/FOXP1/IL4/RB1/FADD/PIK3R1/ITPKB/FBXO7/TESC/NFATC2/TESPA1/PRKCZ/NOTCH2/PTPRC/LEF1/RASGRP1/PRKDC/ZFPM1
## GO:0043312 GM2A/DEFA4/SLPI/TARM1/CLEC5A/MPO/GDI2/SIRPA/AZU1/TNFRSF1B/DYNC1H1/ABCA13/PSMB7/FCN1/LTF/DOCK2/PRG3/DNAJC3/PSMA2/ATP11A/AMPD3/LAIR1/GLB1/RAB31/GSN/GPI/ANO6/CREG1/CD63/PLAUR/CAB39/ADAM8/NFAM1/STK10/CAP1/TMEM63A/UBR4/CRISPLD2/CLEC4C/SLC2A5/AP1M1/HK3/GYG1/ABR/CD59/DSC1/CAMP/KCNAB2/DGAT1/MCEMP1/EPX/PTPRC/PRG2/ITGAL/ARSB/COTL1/PTPRJ/RAB5C/PTAFR/GUSB/CMTM6/PGM1/CTSB/RAB37
## GO:0002283 GM2A/DEFA4/SLPI/TARM1/CLEC5A/MPO/GDI2/SIRPA/AZU1/TNFRSF1B/DYNC1H1/ABCA13/PSMB7/FCN1/LTF/DOCK2/PRG3/DNAJC3/PSMA2/ATP11A/AMPD3/LAIR1/GLB1/RAB31/GSN/GPI/ANO6/CREG1/CD63/PLAUR/CAB39/ADAM8/NFAM1/STK10/CAP1/TMEM63A/UBR4/CRISPLD2/CLEC4C/SLC2A5/AP1M1/HK3/GYG1/ABR/CD59/DSC1/CAMP/KCNAB2/DGAT1/MCEMP1/EPX/PTPRC/PRG2/ITGAL/ARSB/COTL1/PTPRJ/RAB5C/PTAFR/GUSB/CMTM6/PGM1/CTSB/RAB37
## Count
## GO:0030099 71
## GO:0045637 45
## GO:1903706 68
## GO:1902105 47
## GO:0043312 64
## GO:0002283 64barplot(ego, showCategory=20)
# based on 1509 genes and 1390 unique genes
pdf(file = file.path(sub.plots.dir, "barplot_GOBP_CRA_CAMP_overlap_genes_genomewide_thresh.pdf"),width = 7, height = 7)
barplot(ego, showCategory=20)
dev.off()## png
## 2# not needed as readable=TRUE in enrichGO function
#egox <- setReadable(ego, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(ego, categorySize="qvalue", foldChange=geneList)## Warning: ggrepel: 10 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
p1 <- cnetplot(ego, categorySize="qvalue", foldChange=geneList)
# for CAMP
coeff.camp <- merge_CG_gw$logFC
names(coeff.camp) <- merge_CG_gw$Gene.x
coeff.camp.df <- data.frame(coeff.camp)
coeff.camp.df$Gene <- names(coeff.camp)
coeff.camp.uniq <- coeff.camp.df$Gene[!is.na(coeff.camp.df$Gene)]
coeff.camp.uniq <- coeff.camp.df[!is.na(coeff.camp.df$Gene), ]
coeff.camp.uniq <- coeff.camp.df[coeff.camp.df$Gene!="NA",]
coeff.camp.uniq <- coeff.camp.df[!duplicated(coeff.camp.df$Gene), ]
coeff.camp.uniq.v <- coeff.camp.uniq$coeff.camp
names(coeff.camp.uniq.v) <- coeff.camp.uniq$Gene
geneList <- coeff.camp.uniq.v
geneList <- sort(geneList, decreasing = TRUE)
entrezid <- names(geneList)
symbols.entrez <- mapIds(org.Hs.eg.db, entrezid, 'ENTREZID', 'SYMBOL')## 'select()' returned 1:1 mapping between keys and columnslength(symbols.entrez)## [1] 1509#ids <- as.numeric(symbols.entrez)
length(unique(symbols.entrez)) # 1390## [1] 1390ids <- lapply(symbols.entrez, as.numeric)
#ids <- as.numeric(symbols.entrez)
names(geneList) <- ids
gene <- names(geneList)
ego <- enrichGO(gene = gene,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
readable = TRUE)
dim(ego)## [1] 251 9head(ego)## ID Description
## GO:0030099 GO:0030099 myeloid cell differentiation
## GO:0045637 GO:0045637 regulation of myeloid cell differentiation
## GO:1903706 GO:1903706 regulation of hemopoiesis
## GO:1902105 GO:1902105 regulation of leukocyte differentiation
## GO:0043312 GO:0043312 neutrophil degranulation
## GO:0002283 GO:0002283 neutrophil activation involved in immune response
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0030099 71/1233 431/18866 4.110661e-13 2.338144e-09 1.981339e-09
## GO:0045637 45/1233 263/18866 2.506735e-09 7.129156e-06 6.041233e-06
## GO:1903706 68/1233 498/18866 5.649299e-09 9.610415e-06 8.143847e-06
## GO:1902105 47/1233 290/18866 6.758379e-09 9.610415e-06 8.143847e-06
## GO:0043312 64/1233 487/18866 6.862848e-08 7.807176e-05 6.615786e-05
## GO:0002283 64/1233 490/18866 8.630413e-08 8.181632e-05 6.933099e-05
## geneID
## GO:0030099 TGFBR2/CLEC5A/TNF/TREM2/LRRK1/APP/UBASH3B/MIR145/LTF/GPR68/IL20/STAT1/STAT3/IL34/THRA/TMOD3/LRRC17/RASSF2/PIP4K2A/RNF41/ASH2L/P4HTM/EPAS1/ADD1/ADAR/EIF6/CD4/PRKCB/KMT2C/CDK6/FARP2/SETD1A/MTURN/FOXP1/TRIB1/SRC/SPI1/HDAC1/ARID4A/RARG/CBFB/CD81/KLF1/FAXDC2/CEBPB/MITF/CEBPE/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/LBR/ACTN1/SH3PXD2A/FADD/BATF2/PIK3R1/CREBBP/CDK5RAP3/KAT8/VPS33A/ITPKB/MFHAS1/TESC/HIPK2/PRKDC/IKZF1/LEF1/ZFPM1
## GO:0045637 TNF/TREM2/UBASH3B/MIR145/LTF/GPR68/IL20/STAT1/STAT3/IL34/LRRC17/RASSF2/RNF41/ASH2L/P4HTM/EIF6/CD4/PRKCB/KMT2C/CDK6/SETD1A/MTURN/FOXP1/TRIB1/SPI1/HDAC1/RARG/CBFB/FAXDC2/CEBPB/MITF/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/FADD/PIK3R1/CREBBP/ITPKB/TESC/PRKDC/LEF1/ZFPM1
## GO:1903706 TGFBR2/ABL1/ZMIZ1/TNF/TREM2/PSMB7/UBASH3B/MIR145/LTF/GPR68/HLX/IL20/STAT1/STAT3/IL1B/IL34/PSMA2/PIK3R6/LRRC17/RASSF2/ITCH/RNF41/ASH2L/P4HTM/ADA/EIF6/CD4/PRKCB/AGER/KMT2C/CDK6/SH3RF1/NFATC2/SETD1A/MTURN/FOXP1/TRIB1/SPI1/HDAC1/PSMC1/RARG/CBFB/TCF7/FAXDC2/CD28/CEBPB/MITF/ADAM8/NFAM1/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/FBXO7/RASGRP1/TESPA1/FADD/PIK3R1/CREBBP/PTPRC/ITPKB/PRKCZ/TESC/PRKDC/LEF1/ZFPM1
## GO:1902105 TGFBR2/ABL1/ZMIZ1/TNF/TREM2/UBASH3B/MIR145/LTF/GPR68/HLX/IL20/IL1B/IL34/PIK3R6/LRRC17/RASSF2/RNF41/ADA/CD4/AGER/CDK6/SH3RF1/NFATC2/FOXP1/TRIB1/CBFB/TCF7/CD28/CEBPB/MITF/ADAM8/NFAM1/NOTCH2/RB1/IL4/FBXO7/RASGRP1/TESPA1/FADD/PIK3R1/PTPRC/ITPKB/PRKCZ/TESC/PRKDC/LEF1/ZFPM1
## GO:0043312 TARM1/CLEC5A/GM2A/DEFA4/AZU1/SIRPA/SLPI/MPO/GDI2/ABCA13/DYNC1H1/PSMB7/TNFRSF1B/LTF/FCN1/PRG3/DOCK2/DNAJC3/PSMA2/GLB1/AMPD3/RAB31/GPI/LAIR1/CREG1/PLAUR/ANO6/UBR4/GSN/ATP11A/CAB39/CAP1/AP1M1/STK10/CAMP/KCNAB2/CD59/CD63/GYG1/ADAM8/NFAM1/DGAT1/TMEM63A/CRISPLD2/ITGAL/CLEC4C/SLC2A5/HK3/ABR/PTPRJ/PGM1/RAB5C/DSC1/PTPRC/ARSB/EPX/RAB37/CTSB/CMTM6/MCEMP1/PRG2/PTAFR/COTL1/GUSB
## GO:0002283 TARM1/CLEC5A/GM2A/DEFA4/AZU1/SIRPA/SLPI/MPO/GDI2/ABCA13/DYNC1H1/PSMB7/TNFRSF1B/LTF/FCN1/PRG3/DOCK2/DNAJC3/PSMA2/GLB1/AMPD3/RAB31/GPI/LAIR1/CREG1/PLAUR/ANO6/UBR4/GSN/ATP11A/CAB39/CAP1/AP1M1/STK10/CAMP/KCNAB2/CD59/CD63/GYG1/ADAM8/NFAM1/DGAT1/TMEM63A/CRISPLD2/ITGAL/CLEC4C/SLC2A5/HK3/ABR/PTPRJ/PGM1/RAB5C/DSC1/PTPRC/ARSB/EPX/RAB37/CTSB/CMTM6/MCEMP1/PRG2/PTAFR/COTL1/GUSB
## Count
## GO:0030099 71
## GO:0045637 45
## GO:1903706 68
## GO:1902105 47
## GO:0043312 64
## GO:0002283 64barplot(ego, showCategory=20)
#dotplot(ego)
enrichplot::dotplot(ego, showCategory=30) + ggtitle("dotplot for GO ORA")## wrong orderBy parameter; set to default `orderBy = "x"`
#gseaplot(y, y[1,1], title=y[1,2])
pdf(file = file.path(sub.plots.dir, "dotplot_enrichGO_CRA_CAMP.pdf"),width = 7, height = 7)
enrichplot::dotplot(ego, showCategory=20) + ggtitle("dotplot for GO ORA")## wrong orderBy parameter; set to default `orderBy = "x"`dev.off()## png
## 2egox <- setReadable(ego, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(ego, categorySize="qvalue", foldChange=geneList)## Warning: ggrepel: 30 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
p2 <- cnetplot(ego, categorySize="qvalue", foldChange=geneList)
# for better visualizing chose nrow=2
cowplot::plot_grid(p1, p2, ncol=1, nrow=2,labels=LETTERS[1:2], rel_widths=c(.8, .8))## Warning: ggrepel: 118 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps## Warning: ggrepel: 132 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
pdf(file = file.path(sub.plots.dir, "clusterProfiler_enrichGO_CRA_CAMP_coeff_overlap_univ.pdf"),width = 22, height = 9)
# Genes and gene ontology enrichments network
cowplot::plot_grid(p1, p2, ncol=2, labels=LETTERS[1:2], rel_widths=c(.8, .8))
dev.off()## png
## 2# Can also plot it this way as both plots would anyway look same except fold change in both datasets
# without fold change
cnetplot(ego, node_label="all", categorySize="qvalue")## Warning: ggrepel: 26 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
# save it
pdf(file = file.path(sub.plots.dir, "clusterProfiler_enrichGO_CRA_CAMP_overlap_without_coeff.pdf"),width = 11, height = 9)
# Genes and gene ontology enrichments network
cnetplot(ego, node_label="all", categorySize="qvalue")
dev.off()## png
## 2# Enrichment map organizes enriched terms into a network with edges connecting overlapping gene sets. In this way, mutually overlapping gene sets are tend to cluster together, making it easy to identify functional module
# the plot would look same for CRA and CAMP as you are just plotting pvalues and terms, not the effect estimates
x1 <- pairwise_termsim(ego)
emapplot(x1)
pdf(file = file.path(sub.plots.dir, "enrichmentMap_pairwise_enrichGO_CRA_CAMP_overlap_gw_genes.pdf"),
width = 11, height = 9)
emapplot(x1)
dev.off()## png
## 2kk <- enrichKEGG(gene = gene,
organism = 'hsa',
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
qvalueCutoff = 0.05,
minGSSize = 50,
maxGSSize = 500)## Reading KEGG annotation online:## Reading KEGG annotation online:dim(kk) #28## [1] 29 9kk.ge <- setReadable(kk, 'org.Hs.eg.db', 'ENTREZID')
head(kk.ge)## ID Description GeneRatio
## hsa04070 hsa04070 Phosphatidylinositol signaling system 24/620
## hsa04921 hsa04921 Oxytocin signaling pathway 28/620
## hsa04725 hsa04725 Cholinergic synapse 21/620
## hsa04750 hsa04750 Inflammatory mediator regulation of TRP channels 19/620
## hsa04371 hsa04371 Apelin signaling pathway 23/620
## hsa00562 hsa00562 Inositol phosphate metabolism 15/620
## BgRatio pvalue p.adjust qvalue
## hsa04070 97/8113 1.707659e-07 3.978845e-05 2.876057e-05
## hsa04921 154/8113 1.255423e-05 1.462568e-03 1.057198e-03
## hsa04725 113/8113 1.091982e-04 7.481291e-03 5.407755e-03
## hsa04750 98/8113 1.284342e-04 7.481291e-03 5.407755e-03
## hsa04371 139/8113 3.196988e-04 1.286082e-02 9.296278e-03
## hsa00562 73/8113 3.356060e-04 1.286082e-02 9.296278e-03
## geneID
## hsa04070 ITPR2/SYNJ2/PIK3C2B/ITPKC/CALML4/PTEN/PI4KA/INPP5F/PIP4K2A/PIP5K1B/PRKCB/PI4KB/PIK3CB/DGKI/IP6K2/ITPK1/INPP5A/CALM1/DGKG/PIK3R1/ITPKB/INPP4A/ITPR1/MTMR3
## hsa04921 CAMKK2/ITPR2/ADCY9/CACNA2D2/CALML4/GNAQ/MYLK4/PIK3R6/KCNJ6/MAP2K5/CACNA2D1/PRKCB/CACNA1S/NFATC2/PRKAG2/CAMK1D/SRC/CACNA1D/MYLK/PRKAB1/PIK3R5/MYL9/CALM1/EEF2K/GNAO1/CAMK2G/ITPR1/MYLK3
## hsa04725 ITPR2/ADCY9/CREB3L4/GNG7/GNAQ/CREB3L2/PIK3R6/KCNJ6/CHRM1/PRKCB/CACNA1S/PIK3CB/GNG12/CACNA1D/GNB5/PIK3R5/PIK3R1/FYN/GNAO1/CAMK2G/ITPR1
## hsa04750 NGF/ITPR2/ADCY9/CALML4/IL1B/GNAQ/PRKCE/BDKRB2/PRKCB/MAPK13/PIK3CB/SRC/ASIC1/P2RY2/CALM1/PIK3R1/CAMK2G/ITPR1/PRKCH
## hsa04371 ITPR2/ADCY9/CALML4/GNG7/GNAQ/MYLK4/PIK3R6/PRKCE/GNG12/PRKAG2/MYLK/PRKAB1/GNB5/PIK3R5/JAG1/CALM1/MAP1LC3B2/MEF2D/HDAC4/SPHK2/ITPR1/CDH1/MYLK3
## hsa00562 SYNJ2/PIK3C2B/ITPKC/PTEN/PI4KA/INPP5F/PIP4K2A/PIP5K1B/PI4KB/PIK3CB/ITPK1/INPP5A/ITPKB/INPP4A/MTMR3
## Count
## hsa04070 24
## hsa04921 28
## hsa04725 21
## hsa04750 19
## hsa04371 23
## hsa00562 15# shows all enriched KEGG terms
kk.ge@result$Description## [1] "Phosphatidylinositol signaling system"
## [2] "Oxytocin signaling pathway"
## [3] "Cholinergic synapse"
## [4] "Inflammatory mediator regulation of TRP channels"
## [5] "Apelin signaling pathway"
## [6] "Inositol phosphate metabolism"
## [7] "Dopaminergic synapse"
## [8] "Kaposi sarcoma-associated herpesvirus infection"
## [9] "Aldosterone synthesis and secretion"
## [10] "Insulin resistance"
## [11] "Calcium signaling pathway"
## [12] "Axon guidance"
## [13] "Human cytomegalovirus infection"
## [14] "cGMP-PKG signaling pathway"
## [15] "Adherens junction"
## [16] "Platelet activation"
## [17] "Hepatitis B"
## [18] "Insulin signaling pathway"
## [19] "Sphingolipid signaling pathway"
## [20] "Glioma"
## [21] "AMPK signaling pathway"
## [22] "GnRH signaling pathway"
## [23] "Gastric acid secretion"
## [24] "T cell receptor signaling pathway"
## [25] "Lysosome"
## [26] "Endocytosis"
## [27] "Focal adhesion"
## [28] "Amphetamine addiction"
## [29] "Chemokine signaling pathway"
## [30] "Cellular senescence"
## [31] "Yersinia infection"
## [32] "Osteoclast differentiation"
## [33] "Growth hormone synthesis, secretion and action"
## [34] "Hepatocellular carcinoma"
## [35] "Melanogenesis"
## [36] "Human immunodeficiency virus 1 infection"
## [37] "Viral carcinogenesis"
## [38] "Serotonergic synapse"
## [39] "Renin secretion"
## [40] "Renal cell carcinoma"
## [41] "Glucagon signaling pathway"
## [42] "Glycerolipid metabolism"
## [43] "GABAergic synapse"
## [44] "Rap1 signaling pathway"
## [45] "Endocrine and other factor-regulated calcium reabsorption"
## [46] "HIF-1 signaling pathway"
## [47] "Neurotrophin signaling pathway"
## [48] "AGE-RAGE signaling pathway in diabetic complications"
## [49] "Adrenergic signaling in cardiomyocytes"
## [50] "Autophagy - animal"
## [51] "FoxO signaling pathway"
## [52] "Shigellosis"
## [53] "TNF signaling pathway"
## [54] "Cortisol synthesis and secretion"
## [55] "Vascular smooth muscle contraction"
## [56] "Regulation of actin cytoskeleton"
## [57] "C-type lectin receptor signaling pathway"
## [58] "Cushing syndrome"
## [59] "Carbon metabolism"
## [60] "Pancreatic cancer"
## [61] "Glycolysis / Gluconeogenesis"
## [62] "Cell cycle"
## [63] "Fc gamma R-mediated phagocytosis"
## [64] "Circadian entrainment"
## [65] "Prostate cancer"
## [66] "Fc epsilon RI signaling pathway"
## [67] "Estrogen signaling pathway"
## [68] "Notch signaling pathway"
## [69] "Longevity regulating pathway"
## [70] "Hypertrophic cardiomyopathy"
## [71] "Thyroid hormone signaling pathway"
## [72] "Spinocerebellar ataxia"
## [73] "Non-small cell lung cancer"
## [74] "Wnt signaling pathway"
## [75] "Leukocyte transendothelial migration"
## [76] "GnRH secretion"
## [77] "Inflammatory bowel disease"
## [78] "Parathyroid hormone synthesis, secretion and action"
## [79] "Insulin secretion"
## [80] "Chronic myeloid leukemia"
## [81] "Relaxin signaling pathway"
## [82] "Bacterial invasion of epithelial cells"
## [83] "Long-term potentiation"
## [84] "Acute myeloid leukemia"
## [85] "Human papillomavirus infection"
## [86] "Glycerophospholipid metabolism"
## [87] "Endometrial cancer"
## [88] "Oocyte meiosis"
## [89] "PD-L1 expression and PD-1 checkpoint pathway in cancer"
## [90] "Ras signaling pathway"
## [91] "VEGF signaling pathway"
## [92] "Biosynthesis of cofactors"
## [93] "mTOR signaling pathway"
## [94] "N-Glycan biosynthesis"
## [95] "Amoebiasis"
## [96] "Tuberculosis"
## [97] "Salivary secretion"
## [98] "Longevity regulating pathway - multiple species"
## [99] "Lysine degradation"
## [100] "ErbB signaling pathway"
## [101] "Dilated cardiomyopathy"
## [102] "Thyroid hormone synthesis"
## [103] "Colorectal cancer"
## [104] "cAMP signaling pathway"
## [105] "Ubiquitin mediated proteolysis"
## [106] "Alcoholic liver disease"
## [107] "Endocrine resistance"
## [108] "MAPK signaling pathway"
## [109] "Fatty acid metabolism"
## [110] "EGFR tyrosine kinase inhibitor resistance"
## [111] "Breast cancer"
## [112] "Adipocytokine signaling pathway"
## [113] "Pancreatic secretion"
## [114] "Chagas disease"
## [115] "Morphine addiction"
## [116] "Phospholipase D signaling pathway"
## [117] "Retrograde endocannabinoid signaling"
## [118] "Glutamatergic synapse"
## [119] "Th1 and Th2 cell differentiation"
## [120] "Small cell lung cancer"
## [121] "Prolactin signaling pathway"
## [122] "PI3K-Akt signaling pathway"
## [123] "Human T-cell leukemia virus 1 infection"
## [124] "Melanoma"
## [125] "Alcoholism"
## [126] "Chemical carcinogenesis - receptor activation"
## [127] "MicroRNAs in cancer"
## [128] "Epstein-Barr virus infection"
## [129] "Transcriptional misregulation in cancer"
## [130] "Hippo signaling pathway"
## [131] "Gap junction"
## [132] "Leishmaniasis"
## [133] "Arrhythmogenic right ventricular cardiomyopathy"
## [134] "Influenza A"
## [135] "Progesterone-mediated oocyte maturation"
## [136] "Salmonella infection"
## [137] "Pathways of neurodegeneration - multiple diseases"
## [138] "B cell receptor signaling pathway"
## [139] "Proteoglycans in cancer"
## [140] "Long-term depression"
## [141] "Viral myocarditis"
## [142] "Hepatitis C"
## [143] "NOD-like receptor signaling pathway"
## [144] "Choline metabolism in cancer"
## [145] "Malaria"
## [146] "Basal cell carcinoma"
## [147] "Toxoplasmosis"
## [148] "Purine metabolism"
## [149] "Bile secretion"
## [150] "Fluid shear stress and atherosclerosis"
## [151] "Protein digestion and absorption"
## [152] "Alzheimer disease"
## [153] "Signaling pathways regulating pluripotency of stem cells"
## [154] "Drug metabolism - other enzymes"
## [155] "Hedgehog signaling pathway"
## [156] "TGF-beta signaling pathway"
## [157] "IL-17 signaling pathway"
## [158] "Peroxisome"
## [159] "Central carbon metabolism in cancer"
## [160] "Glutathione metabolism"
## [161] "mRNA surveillance pathway"
## [162] "Apoptosis"
## [163] "Gastric cancer"
## [164] "JAK-STAT signaling pathway"
## [165] "Complement and coagulation cascades"
## [166] "Lipid and atherosclerosis"
## [167] "Neutrophil extracellular trap formation"
## [168] "Hematopoietic cell lineage"
## [169] "Viral protein interaction with cytokine and cytokine receptor"
## [170] "Cardiac muscle contraction"
## [171] "Arachidonic acid metabolism"
## [172] "Biosynthesis of amino acids"
## [173] "Prion disease"
## [174] "Tight junction"
## [175] "Cholesterol metabolism"
## [176] "Toll-like receptor signaling pathway"
## [177] "Natural killer cell mediated cytotoxicity"
## [178] "Ovarian steroidogenesis"
## [179] "Synaptic vesicle cycle"
## [180] "Th17 cell differentiation"
## [181] "Measles"
## [182] "RIG-I-like receptor signaling pathway"
## [183] "Regulation of lipolysis in adipocytes"
## [184] "Non-alcoholic fatty liver disease"
## [185] "Huntington disease"
## [186] "Mitophagy - animal"
## [187] "Platinum drug resistance"
## [188] "Cytokine-cytokine receptor interaction"
## [189] "Mineral absorption"
## [190] "PPAR signaling pathway"
## [191] "NF-kappa B signaling pathway"
## [192] "Diabetic cardiomyopathy"
## [193] "Pertussis"
## [194] "Thermogenesis"
## [195] "Cytosolic DNA-sensing pathway"
## [196] "Rheumatoid arthritis"
## [197] "Cysteine and methionine metabolism"
## [198] "Protein processing in endoplasmic reticulum"
## [199] "Necroptosis"
## [200] "Drug metabolism - cytochrome P450"
## [201] "ECM-receptor interaction"
## [202] "Cell adhesion molecules"
## [203] "Legionellosis"
## [204] "Pyrimidine metabolism"
## [205] "Steroid hormone biosynthesis"
## [206] "Antigen processing and presentation"
## [207] "Staphylococcus aureus infection"
## [208] "Chemical carcinogenesis - reactive oxygen species"
## [209] "Aminoacyl-tRNA biosynthesis"
## [210] "Pathogenic Escherichia coli infection"
## [211] "Chemical carcinogenesis - DNA adducts"
## [212] "Arginine and proline metabolism"
## [213] "Epithelial cell signaling in Helicobacter pylori infection"
## [214] "Parkinson disease"
## [215] "Autoimmune thyroid disease"
## [216] "p53 signaling pathway"
## [217] "Metabolism of xenobiotics by cytochrome P450"
## [218] "RNA degradation"
## [219] "Nucleocytoplasmic transport"
## [220] "Retinol metabolism"
## [221] "Ribosome biogenesis in eukaryotes"
## [222] "Amyotrophic lateral sclerosis"
## [223] "Vibrio cholerae infection"
## [224] "Coronavirus disease - COVID-19"
## [225] "Fanconi anemia pathway"
## [226] "Phagosome"
## [227] "Systemic lupus erythematosus"
## [228] "Spliceosome"
## [229] "Taste transduction"
## [230] "Neuroactive ligand-receptor interaction"
## [231] "Oxidative phosphorylation"
## [232] "Herpes simplex virus 1 infection"
## [233] "Olfactory transduction"save(kk.ge, file=file.path(res.dir,
paste0("enrich_Kegg_CRA_CAMP_genomewide_thresh_", timeStamp, ".RData")))
write.table(kk.ge@result,file=file.path(res.dir,
paste0("enrichKegg_CRA_CAMP_gw_thresh_",timeStamp,".txt"))
,sep="\t",row.names=F,quote=F)
browseKEGG(kk, 'hsa04070')
library("pathview")## ##############################################################################
## Pathview is an open source software package distributed under GNU General
## Public License version 3 (GPLv3). Details of GPLv3 is available at
## http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
## formally cite the original Pathview paper (not just mention it) in publications
## or products. For details, do citation("pathview") within R.
##
## The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
## license agreement (details at http://www.kegg.jp/kegg/legal.html).
## ##############################################################################hsa04070 <- pathview(gene.data = geneList,
pathway.id = "hsa04070",
species = "hsa",
limit = list(gene=max(abs(geneList)), cpd=1))## 'select()' returned 1:1 mapping between keys and columns## Info: Working in directory /udd/reprk/projects/TOPMed/scripts## Info: Writing image file hsa04070.pathview.pngfile.copy("hsa04070.pathview.png", sub.plots.dir)## [1] FALSE#eg2np <- bitr_kegg(gene, fromType='kegg', toType='ncbi-geneid', organism='hsa')
geneList.na <- geneList[names(geneList)!="NA"]
kk2 <- gseKEGG(geneList = geneList.na,
organism = 'hsa',
minGSSize = 50,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
maxGSSize = 500,
by = "fgsea",
verbose = TRUE)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...head(kk2)## [1] ID Description setSize enrichmentScore
## [5] NES pvalue p.adjust qvalues
## <0 rows> (or 0-length row.names)#preparing geneSet collections...
#GSEA analysis...
#no term enriched under specific pvalueCutoff...
# GSEA , no enrichment
ego.gse <- gseGO(geneList = geneList.na,
OrgDb = org.Hs.eg.db,
ont = "BP",
minGSSize = 50,
maxGSSize = 500,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
verbose = TRUE)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...# H and C2,3,5,7,8
# Gene set enrichment analysis
msigdbr_show_species()## Warning: 'msigdbr_show_species' is deprecated.
## Use 'msigdbr_species' instead.
## See help("Deprecated")## [1] "Anolis carolinensis" "Bos taurus"
## [3] "Caenorhabditis elegans" "Canis lupus familiaris"
## [5] "Danio rerio" "Drosophila melanogaster"
## [7] "Equus caballus" "Felis catus"
## [9] "Gallus gallus" "Homo sapiens"
## [11] "Macaca mulatta" "Monodelphis domestica"
## [13] "Mus musculus" "Ornithorhynchus anatinus"
## [15] "Pan troglodytes" "Rattus norvegicus"
## [17] "Saccharomyces cerevisiae" "Schizosaccharomyces pombe 972h-"
## [19] "Sus scrofa" "Xenopus tropicalis"m_df <- msigdbr(species = "Homo sapiens")
head(m_df, 2) %>% as.data.frame## gs_cat gs_subcat gs_name gene_symbol entrez_gene ensembl_gene
## 1 C3 MIR:MIR_Legacy AAACCAC_MIR140 ABCC4 10257 ENSG00000125257
## 2 C3 MIR:MIR_Legacy AAACCAC_MIR140 ABRAXAS2 23172 ENSG00000165660
## human_gene_symbol human_entrez_gene human_ensembl_gene gs_id gs_pmid
## 1 ABCC4 10257 ENSG00000125257 M12609
## 2 ABRAXAS2 23172 ENSG00000165660 M12609
## gs_geoid gs_exact_source gs_url
## 1
## 2
## gs_description
## 1 Genes having at least one occurence of the motif AAACCAC in their 3' untranslated region. The motif represents putative target (that is, seed match) of human mature miRNA hsa-miR-140 (v7.1 miRBase).
## 2 Genes having at least one occurence of the motif AAACCAC in their 3' untranslated region. The motif represents putative target (that is, seed match) of human mature miRNA hsa-miR-140 (v7.1 miRBase).# Pulling data from msigdbr
# hallmark gene sets
m_H <- msigdbr(species = "Homo sapiens", category = "H") %>%
dplyr::select(gs_name, entrez_gene)
# curated gene sets
m_C2 <- msigdbr(species = "Homo sapiens", category = "C2") %>%
dplyr::select(gs_name, entrez_gene)
# regulatory target/motif gene sets
m_C3 <- msigdbr(species = "Homo sapiens", category = "C3") %>%
dplyr::select(gs_name, entrez_gene)
# ontology gene sets
m_C5 <- msigdbr(species = "Homo sapiens", category = "C5") %>%
dplyr::select(gs_name, entrez_gene)
# immunologic signature gene sets
m_C7 <- msigdbr(species = "Homo sapiens", category = "C7") %>%
dplyr::select(gs_name, entrez_gene)
# cell type signature gene sets
m_C8 <- msigdbr(species = "Homo sapiens", category = "C8") %>%
dplyr::select(gs_name, entrez_gene)
# enrichments
em.H <- enricher(gene, TERM2GENE=m_H, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # not sig
dim(em.H)## [1] 0 9em.C2 <- enricher(gene, TERM2GENE=m_C2, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 563
em.C2.ge <- setReadable(em.C2, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C2.ge)## [1] 563 9head(em.C2.ge)## ID
## MARTENS_BOUND_BY_PML_RARA_FUSION MARTENS_BOUND_BY_PML_RARA_FUSION
## GRYDER_PAX3FOXO1_TOP_ENHANCERS GRYDER_PAX3FOXO1_TOP_ENHANCERS
## ZHENG_BOUND_BY_FOXP3 ZHENG_BOUND_BY_FOXP3
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY WP_VEGFAVEGFR2_SIGNALING_PATHWAY
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP
## Description
## MARTENS_BOUND_BY_PML_RARA_FUSION MARTENS_BOUND_BY_PML_RARA_FUSION
## GRYDER_PAX3FOXO1_TOP_ENHANCERS GRYDER_PAX3FOXO1_TOP_ENHANCERS
## ZHENG_BOUND_BY_FOXP3 ZHENG_BOUND_BY_FOXP3
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY WP_VEGFAVEGFR2_SIGNALING_PATHWAY
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP
## GeneRatio BgRatio pvalue
## MARTENS_BOUND_BY_PML_RARA_FUSION 89/1333 455/21697 7.945626e-23
## GRYDER_PAX3FOXO1_TOP_ENHANCERS 71/1333 441/21697 7.264148e-14
## ZHENG_BOUND_BY_FOXP3 75/1333 495/21697 3.467969e-13
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY 68/1333 438/21697 1.421528e-12
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN 43/1333 227/21697 3.222204e-11
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP 61/1333 412/21697 1.495306e-10
## p.adjust qvalue
## MARTENS_BOUND_BY_PML_RARA_FUSION 3.883822e-19 2.993410e-19
## GRYDER_PAX3FOXO1_TOP_ENHANCERS 1.775358e-10 1.368336e-10
## ZHENG_BOUND_BY_FOXP3 5.650478e-10 4.355040e-10
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY 1.737107e-09 1.338855e-09
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN 3.150026e-08 2.427846e-08
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP 1.218176e-07 9.388948e-08
## geneID
## MARTENS_BOUND_BY_PML_RARA_FUSION ZMIZ1/CUX1/UCK2/CELF2/SIRPA/RHBDF2/ITPR2/ANKRD11/UBASH3B/TPD52L2/FCN1/PTEN/HNRNPM/PITPNM2/KLHL24/WNT5B/IQCD/ST3GAL2/ABHD2/RAB31/NCOR2/CCDC174/CHST15/SLC24A3/ALOX5AP/ACSL1/IQSEC1/PREX1/HCK/PIGL/PAFAH2/SPI1/RAB20/RPS6KA2/GSE1/PHF12/RNF122/NOLC1/GAS7/GALC/EFHD2/PIK3AP1/KCNAB2/NDRG1/RAB11FIP1/GNB5/ANKRD33B/ADAM8/ALDH2/PEBP4/MYO9B/POC1A/RNF34/MBD6/TBXAS1/UBE2O/WDR81/CDH23/P2RY2/ADORA3/LBR/RAP1GAP2/TMEM104/PXN/FAM53B/RAPGEF1/DENND3/SH3PXD2A/SULF2/MEF2D/PTPRJ/HDAC4/SPTBN1/NADK/GALNT6/SPHK2/GFOD1/RAB37/CAMK2G/ACP5/TESC/ITPR1/LRRC20/MGLL/CAPG/COTL1/DAPK2/GUSB/KSR1
## GRYDER_PAX3FOXO1_TOP_ENHANCERS CELF2/TNS3/PPM1H/CHST11/GDI2/ADCY9/TGOLN2/ADAM19/APP/RBM20/ARHGEF10/JARID2/ANKRD13A/CLASP1/MFSD2A/HMGXB4/CHCHD3/PARK7/COL4A1/MCC/OPA1/ZEB2/SPATS2L/COPS3/NR3C1/VTI1A/SUDS3/MAN1C1/CEP128/MED13L/NCOR2/UBAC2/CHST15/SLC24A3/ALOX5AP/SNX29/CD9/PLXNA2/POR/PREX1/ARHGAP26/GSE1/CAP1/NOLC1/EFHD2/NOTCH2/ADAMTS14/MYO9B/CSRP1/SLC7A1/MCM2/LRIG1/ELMO1/USP15/RAPGEF1/RERE/CTNNBL1/EEF2K/SULF2/STIM2/SASH1/CREBBP/ITPKB/TRAP1/GGA2/TLE3/FYN/GRB10/MSI2/DAPK1/SNX9
## ZHENG_BOUND_BY_FOXP3 TGFBR2/CELF2/MGAT5/TRIM27/PPP2R5C/GDI2/ITPR2/OPRM1/SSH2/ADAM19/ANKRD11/UBASH3B/ARHGEF10/JARID2/EXT1/PARK7/ZNRF1/HECTD1/LRRC8C/IL10RB/SRPK1/PIP4K2A/VGLL4/ZNF175/PDE4B/UST/AGPS/PHTF2/LDLRAD4/ABTB2/UBAC2/DENND5A/STAT4/THADA/FOXP1/LCP1/TRIB1/STK10/IKZF2/RAB19/SAG/EPS15L1/TET3/EPB41/IBTK/RBL2/CD28/NCK2/PEBP4/PTK2B/INTS9/AKAP13/RB1/MAP4K4/GPD2/LRIG1/SGMS1/XXYLT1/ELMO1/CYTH1/HK3/TESPA1/MUC20/PTPRC/SPTBN1/VOPP1/FYN/TBC1D5/GPHN/CDK17/MAP3K1/LEF1/SNX9/PRKCH/SLC23A2
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY CAMKK2/ABL1/VAV2/TPP1/ACACA/MKNK1/CCRL2/HLX/STAT1/STAT3/KL/HDAC9/EPHB2/CDC42BPB/TMOD3/SRPK1/ITCH/NAPA/EPS15/CAPZB/VPS39/MICAL2/PTPN1/CACNA2D1/PRKCE/TPCN2/PRKCB/TNXB/SIAH2/BRD4/PLAUR/NFATC2/GRB2/SRC/NOTCH4/HDAC1/LRRC59/BSG/CHAC1/CAPN2/EPB41/NDRG1/TPM3/PTK2B/CSRP1/SLC7A1/ERG/JAG1/LDB2/TKT/TMOD1/PXN/EIF4G2/MLST8/RAPGEF1/FADD/PTPRJ/FHL2/PIK3R1/CREBBP/DSC1/HDAC4/FYN/GRB10/RAB37/PRKCZ/SLC25A25/ENG
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN CELF2/TRIM27/UBN1/GDI2/LRRFIP1/RALBP1/RALY/SRPK2/DOCK2/GNAQ/TOPBP1/PPFIA1/CAPZB/TGFA/FKBP1A/PRKCB/PNN/ACTN4/ARID4A/PHKB/GAS7/RBL2/MYO9B/TKT/CALM1/LBR/CYTH1/USP15/EIF4G2/ACTN1/RERE/ENTPD1/SLC19A1/FADD/SELPLG/NCF4/CREBBP/ITPKB/GNAO1/CAMK2G/MTMR3/DAPK2/SLC23A2
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP NEDD9/EPB41L3/CLEC5A/SLC7A7/GM2A/TNS3/SPARC/PCK2/CCRL2/CPM/FCN1/TMEM51/CALML4/STAT1/PHACTR1/ACO1/IL1B/PACSIN2/HDAC9/TRAF3/NPL/SLC7A11/SLC36A1/BCAT1/DHCR24/PRKCB/TBC1D1/LAIR1/CHST15/IDO1/CD9/LTBP2/RAB20/TLE4/CD81/GALC/RSAD2/NDRG1/CD63/CCL18/MITF/NOTCH2/ITPK1/ST3GAL1/ITGAL/GPD2/SGMS1/RAP1GAP2/RERE/DENND3/ENTPD1/OSBPL1A/KCNMA1/MFHAS1/FYN/HK2/MAN2A2/ACP5/CTSB/ITPR1/FBP1
## Count
## MARTENS_BOUND_BY_PML_RARA_FUSION 89
## GRYDER_PAX3FOXO1_TOP_ENHANCERS 71
## ZHENG_BOUND_BY_FOXP3 75
## WP_VEGFAVEGFR2_SIGNALING_PATHWAY 68
## THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN 43
## RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP 61em.C3 <- enricher(gene, TERM2GENE=m_C3, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 1522
em.C3.ge <- setReadable(em.C3, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C3.ge)## [1] 1522 9head(em.C3.ge)## ID Description GeneRatio
## MIR149_3P MIR149_3P MIR149_3P 63/1362
## MIR6883_5P MIR6883_5P MIR6883_5P 60/1362
## MIR4441 MIR4441 MIR4441 48/1362
## MIR6722_3P MIR6722_3P MIR6722_3P 35/1362
## EBNA1BP2_TARGET_GENES EBNA1BP2_TARGET_GENES EBNA1BP2_TARGET_GENES 52/1362
## MIR4755_5P MIR4755_5P MIR4755_5P 49/1362
## BgRatio pvalue p.adjust qvalue
## MIR149_3P 435/28103 7.690761e-15 2.372777e-11 1.083485e-11
## MIR6883_5P 407/28103 1.510361e-14 2.372777e-11 1.083485e-11
## MIR4441 296/28103 1.840739e-13 1.927868e-10 8.803255e-11
## MIR6722_3P 183/28103 2.795053e-12 2.195514e-09 1.002542e-09
## EBNA1BP2_TARGET_GENES 373/28103 7.637394e-12 4.799338e-09 2.191530e-09
## MIR4755_5P 365/28103 1.181133e-10 6.185198e-08 2.824357e-08
## geneID
## MIR149_3P XYLT1/TRIM67/IFFO2/PIK3C2B/KIF21B/TNS1/SUFU/RALB/ATP2A3/HK1/PITPNM2/RFT1/HMGXB3/PEX2/CREB3L2/ERI3/FAIM2/GGCX/CAPZB/DESI1/DEPDC5/NCOR2/COL11A2/SLC22A23/RSPO4/AGPAT1/TPCN1/SREBF2/FOXK1/IQSEC1/YWHAQ/SLC12A4/RPS6KA2/FAM131B/ARNT2/RTN3/ASIC1/TET3/MDM4/MINK1/RPH3AL/RNF24/SLC7A1/SH3GL1/RASSF5/CSDE1/MTA2/UNC5B/RAP1GAP2/TMEM104/SSBP3/SDC3/MEF2D/PTPRJ/STIM1/SOGA1/ANKRD52/NGFR/RAB37/AHDC1/GNAO1/HIPK2/TTYH3
## MIR6883_5P XYLT1/TRIM67/IFFO2/PIK3C2B/KIF21B/TNS1/SUFU/RALB/ATP2A3/HK1/PITPNM2/RFT1/HMGXB3/CREB3L2/ERI3/FAIM2/GGCX/CAPZB/DESI1/DEPDC5/NCOR2/COL11A2/SLC22A23/RSPO4/AGPAT1/TPCN1/SREBF2/FOXK1/IQSEC1/YWHAQ/SLC12A4/RPS6KA2/FAM131B/ARNT2/RTN3/ASIC1/TET3/MINK1/RPH3AL/RNF24/SLC7A1/SH3GL1/RASSF5/CSDE1/MTA2/UNC5B/RAP1GAP2/TMEM104/SSBP3/SDC3/MEF2D/PTPRJ/STIM1/SOGA1/ANKRD52/NGFR/AHDC1/GNAO1/HIPK2/TTYH3
## MIR4441 LRRC27/TPP1/OPRM1/ADAM19/SYNJ2/IFFO2/MYO18A/SUFU/ZBTB34/ZNRF1/MYLK4/SAMD4B/RAB3B/TOM1L2/ZDHHC3/CAPZB/LARP1/SLC41A1/NXF1/CSNK1D/ABHD2/ERC1/RPH3A/COL11A2/PLXNA2/FOXK1/MTUS2/TET3/ADARB1/MITF/ZNF70/SLC7A6/NFAM1/RNF24/APBA2/RCC2/P2RY2/ELMO1/RAP1GAP2/RAPGEF1/PCYT1A/SDC3/MEF2D/SOGA1/SLC4A5/GNAO1/FADS2/IKZF1
## MIR6722_3P TGFBR2/ADCY9/RBM20/KIF21B/GRAMD1B/RNF157/SIPA1L3/XPO7/CREB3L2/AAK1/LHPP/SNX21/C16orf70/C19orf54/CHST15/TXNRD2/NFATC2/TMEM201/RYBP/IP6K2/ARNT2/EFHD2/NFAM1/ITGAL/RERE/UPP2/TRAPPC9/SH3PXD2A/MEF2D/ITPKB/SOGA1/AHDC1/CAMK2G/LRRC20/TTYH3
## EBNA1BP2_TARGET_GENES CUX1/SLC25A37/ITPR2/MOK/ASB1/CACNA2D2/IL20/MTHFD2/HECTD1/TRANK1/SLC2A9/XPO7/UBE2D3/ERI3/INPP5F/CAMKMT/NT5DC3/VTI1A/HCFC1R1/IFT27/LAIR1/IDO1/TXNRD2/CLSTN3/AHNAK/ABCB9/FARP2/SRC/CACNA1D/ACTN4/DIDO1/LAMB1/ABCC1/DNAJC6/RSAD2/DAG1/IGF1R/C16orf72/ENO3/C11orf24/UXS1/SEMA4D/GPATCH1/STIM1/ITPKB/TNFAIP8/PTPRS/LOC101927851/AKAP1/TTC7A/ZBTB48/SLC23A2
## MIR4755_5P TGFBR2/LPP/FBN2/CELF2/ZNF148/ZDHHC14/AFAP1/JARID2/ANKRD13A/RAD21/GNAQ/EPHB2/WDFY2/TMOD3/NR3C1/AK2/ERC1/GSTM3/MTCL1/PI4KB/RSPO4/ANO6/PIK3CB/PLXNA2/GNG12/CAMK1D/SPOP/IKZF2/EPHA4/MGAT3/ENTHD1/CTIF/SNAP47/BCL7A/C16orf72/MLXIP/SLC7A14/CDYL2/CHN2/CCNY/NCOA7/SH3PXD2A/DGKG/KLHL6/KCNMA1/MAN2A2/RREB1/ITPR1/YPEL2
## Count
## MIR149_3P 63
## MIR6883_5P 60
## MIR4441 48
## MIR6722_3P 35
## EBNA1BP2_TARGET_GENES 52
## MIR4755_5P 49em.C5 <- enricher(gene, TERM2GENE=m_C5, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 352
em.C5.ge <- setReadable(em.C5, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C5.ge)## [1] 352 9head(em.C5.ge)## ID
## GOBP_MYELOID_CELL_DIFFERENTIATION GOBP_MYELOID_CELL_DIFFERENTIATION
## GOBP_REGULATION_OF_HEMOPOIESIS GOBP_REGULATION_OF_HEMOPOIESIS
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY
## Description
## GOBP_MYELOID_CELL_DIFFERENTIATION GOBP_MYELOID_CELL_DIFFERENTIATION
## GOBP_REGULATION_OF_HEMOPOIESIS GOBP_REGULATION_OF_HEMOPOIESIS
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY
## GeneRatio BgRatio
## GOBP_MYELOID_CELL_DIFFERENTIATION 70/1264 419/19303
## GOBP_REGULATION_OF_HEMOPOIESIS 62/1264 415/19303
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION 45/1264 258/19303
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION 45/1264 279/19303
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM 64/1264 476/19303
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY 64/1264 480/19303
## pvalue p.adjust
## GOBP_MYELOID_CELL_DIFFERENTIATION 3.364283e-13 3.046359e-09
## GOBP_REGULATION_OF_HEMOPOIESIS 8.695077e-10 3.936696e-06
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION 1.433888e-09 4.327953e-06
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION 1.751493e-08 3.964943e-05
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM 3.142373e-08 5.690837e-05
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY 4.319327e-08 6.518585e-05
## qvalue
## GOBP_MYELOID_CELL_DIFFERENTIATION 2.587665e-09
## GOBP_REGULATION_OF_HEMOPOIESIS 3.343944e-06
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION 3.676288e-06
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION 3.367937e-05
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM 4.833962e-05
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY 5.537074e-05
## geneID
## GOBP_MYELOID_CELL_DIFFERENTIATION TGFBR2/TNF/TREM2/LRRK1/APP/UBASH3B/MIR145/LTF/GPR68/IL20/STAT1/STAT3/IL34/THRA/TMOD3/LRRC17/RASSF2/PIP4K2A/RNF41/ASH2L/P4HTM/EPAS1/ADD1/ADAR/EIF6/CD4/PRKCB/KMT2C/CDK6/FARP2/SETD1A/MTURN/FOXP1/TRIB1/SRC/SPI1/HDAC1/ARID4A/RARG/CBFB/CD81/KLF1/FAXDC2/CEBPB/MITF/CEBPE/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/LBR/ACTN1/SH3PXD2A/FADD/BATF2/PIK3R1/CREBBP/CDK5RAP3/KAT8/VPS33A/ITPKB/MFHAS1/TESC/HIPK2/PRKDC/IKZF1/LEF1/ZFPM1
## GOBP_REGULATION_OF_HEMOPOIESIS TGFBR2/ABL1/ZMIZ1/TNF/TREM2/UBASH3B/MIR145/LTF/GPR68/HLX/IL20/STAT1/STAT3/IL34/PIK3R6/LRRC17/RASSF2/RNF41/ASH2L/P4HTM/ADA/EIF6/CD4/PRKCB/AGER/KMT2C/CDK6/SH3RF1/NFATC2/SETD1A/MTURN/FOXP1/TRIB1/SPI1/HDAC1/RARG/CBFB/TCF7/FAXDC2/CD28/CEBPB/MITF/ADAM8/NFAM1/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/FBXO7/TESPA1/FADD/PIK3R1/CREBBP/PTPRC/ITPKB/PRKCZ/TESC/PRKDC/LEF1/ZFPM1
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION TNF/TREM2/UBASH3B/MIR145/LTF/GPR68/IL20/STAT1/STAT3/IL34/LRRC17/RASSF2/RNF41/ASH2L/P4HTM/EIF6/CD4/PRKCB/KMT2C/CDK6/SETD1A/MTURN/FOXP1/TRIB1/SPI1/HDAC1/RARG/CBFB/FAXDC2/CEBPB/MITF/NOTCH2/PTK2B/RB1/MYL9/IL4/JAG1/FADD/PIK3R1/CREBBP/ITPKB/TESC/PRKDC/LEF1/ZFPM1
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION TGFBR2/ABL1/ZMIZ1/TNF/TREM2/UBASH3B/MIR145/LTF/GPR68/HLX/IL20/IL34/PIK3R6/LRRC17/RASSF2/RNF41/ADA/CD4/AGER/CDK6/SH3RF1/NFATC2/FOXP1/TRIB1/CBFB/TCF7/CD28/CEBPB/MITF/ADAM8/NFAM1/NOTCH2/RB1/IL4/FBXO7/TESPA1/FADD/PIK3R1/PTPRC/ITPKB/PRKCZ/TESC/PRKDC/LEF1/ZFPM1
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM KIF5C/ZMIZ1/KIDINS220/CUX1/ATN1/ZNF148/DYNC1H1/TREM2/PCNT/ANKRD11/TECR/ZC3H14/USP7/MFSD2A/RHOBTB2/HK1/WDR73/WWOX/RMND1/CLIP1/ZEB2/MED12L/PIGN/TRIM8/ASH1L/KANSL1/SPATA5/ADAR/EARS2/RNASEH2C/KMT2C/CCDC174/MED25/NFIA/IQSEC1/ARID1B/VPS53/ARNT2/POLR1C/COASY/DYRK1A/ADARB1/DAG1/RUSC2/IGF1R/KATNB1/RB1/TNIK/WDR81/HNMT/NEDD4L/RERE/TRAPPC9/LMAN2L/KAT8/UBE3B/B3GALNT2/ARID1A/AHDC1/GNAO1/CARS2/PRKDC/BICD2/DOCK8
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY ABL1/ZMIZ1/ATN1/TRIM27/SUFU/RALY/PARK7/WWOX/HDAC9/MED12L/TRIM8/TRERF1/URI1/PRKCB/MED13L/CBFA2T2/NCOR2/KMT2C/SIAH2/BRD4/SAP30L/CREG1/ZXDC/ARID1B/ACTN4/HDAC1/RYBP/SUPT3H/PHF12/TLE4/CBFB/MTA3/PARP9/RBPMS/SMARCC1/DYRK1A/LIMD1/ARID3A/RB1/LDB2/CDYL2/MAML1/MTA2/PXN/ACTN1/MED27/RERE/NCOA7/PDLIM1/FHL2/TADA2B/CREBBP/HDAC4/KAT8/EZH2/DMAP1/TLE3/ARID1A/NR0B2/ZNF653/LPIN1/TGFB1I1/HIPK2/ZFPM1
## Count
## GOBP_MYELOID_CELL_DIFFERENTIATION 70
## GOBP_REGULATION_OF_HEMOPOIESIS 62
## GOBP_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION 45
## GOBP_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION 45
## HP_HYPOPLASIA_OF_THE_CORPUS_CALLOSUM 64
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY 64em.C7 <- enricher(gene, TERM2GENE=m_C7, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 1909
em.C7.ge <- setReadable(em.C7, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C7.ge)## [1] 1909 9head(em.C7.ge)## ID
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP
## GSE29618_BCELL_VS_MONOCYTE_DN GSE29618_BCELL_VS_MONOCYTE_DN
## Description
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP
## GSE29618_BCELL_VS_MONOCYTE_DN GSE29618_BCELL_VS_MONOCYTE_DN
## GeneRatio
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP 44/1340
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP 42/1340
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP 42/1340
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN 37/1340
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP 39/1340
## GSE29618_BCELL_VS_MONOCYTE_DN 39/1340
## BgRatio
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP 200/21341
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP 197/21341
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP 200/21341
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN 175/21341
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP 197/21341
## GSE29618_BCELL_VS_MONOCYTE_DN 200/21341
## pvalue
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP 1.803578e-13
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP 1.933662e-12
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP 3.275419e-12
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN 5.147329e-11
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP 1.261579e-10
## GSE29618_BCELL_VS_MONOCYTE_DN 2.019368e-10
## p.adjust
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP 9.182018e-10
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP 4.922137e-09
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP 5.558385e-09
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN 6.551263e-08
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP 1.284540e-07
## GSE29618_BCELL_VS_MONOCYTE_DN 1.468658e-07
## qvalue
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP 4.770940e-10
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP 2.557522e-09
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP 2.888115e-09
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN 3.404010e-08
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP 6.674417e-08
## GSE29618_BCELL_VS_MONOCYTE_DN 7.631086e-08
## geneID
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP NEDD9/RHBDF2/CHST11/PPP2R5C/GLIPR2/WDFY1/ADCY9/CCRL2/GPR68/ATP2A3/TRANK1/SYTL3/NR3C1/EPS15/GALM/MICAL2/PDE4B/PRKCE/CEP128/CMIP/OGDH/CBFA2T2/C1orf21/JOSD1/CLSTN3/AHNAK/ZNF532/PHF12/CAPN2/ARHGAP10/ADAM8/ANKRD27/TBXAS1/LRIG1/NCOA7/ABR/GABARAPL1/ST3GAL4/SNRNP200/SLCO3A1/GFPT2/FYN/GNAO1/KSR1
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP FKBP9/TGFBR2/SLC25A37/CELF2/PPP2R5C/F5/PTEN/TRANK1/WDFY2/ST3GAL2/ARSG/MICAL2/TRERF1/ZRANB1/MED13L/TBC1D1/SLMAP/ZDHHC18/MTURN/CAMK1D/RYBP/MTMR10/TLE4/RTN3/ARHGAP19/CAMP/RAB11FIP1/NFAM1/DGAT1/TBXAS1/CYTH1/RAP1GAP2/ACTN1/PTPRC/CLC/RAB37/MAN2A2/MTMR3/MAP3K1/BICD2/DOCK8/COTL1
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP TGFBR2/ZMIZ1/LRRFIP1/JARID2/RALB/PTEN/MTHFD2/CCL23/GNAQ/PACSIN2/SWAP70/TMEM156/SLC7A11/SRPK1/CHP1/CHST15/ALOX15/CREG1/PIK3CB/ACSL1/PTPRE/TRIB1/ARHGAP26/GSE1/ADAM8/NOTCH2/RNF24/TKT/PELI2/ACTN1/HK3/GABARAPL1/SELPLG/GFOD1/MCMBP/EPN2/RREB1/LIMK2/CMTM6/PTAFR/EHD1/ZBTB48
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN WDFY4/XYLT1/CELF2/PPM1H/ADAM19/MYO18A/EXT1/ATP2A3/EML3/ACOX1/MICAL1/AMPD3/ABHD2/NFATC2/AHNAK/FOXK1/SPI1/TRIM26/RARG/DMXL1/ANXA6/PRKAB1/DYRK1A/NCK2/MAFK/MYO9B/RNF103/CRTC3/PIK3R5/ENTPD1/XPR1/SH3PXD2A/GALNT6/ARID1A/MTMR3/LPCAT2/TTC7A
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP ABL1/LPP/VDR/TPP1/TNS3/ETV6/EXT1/CLASP1/HMGXB4/STAT1/SPATS2L/BLVRA/KIAA1958/ZDHHC3/ADAR/NEK3/NCOR2/AGPAT1/MYLK/RYBP/MVB12A/CAPN2/GTPBP1/PARP9/CMTR1/PIK3AP1/RSAD2/XAF1/METRNL/TPM3/IFI27/RCC2/NCOA7/SASH1/DENND1A/GALNT6/MAN2A2/MGLL/KSR1
## GSE29618_BCELL_VS_MONOCYTE_DN ZMIZ1/EPB41L3/SLC7A7/TPP1/SVIL/TPD52L2/EXT1/CALML4/GNAQ/NPL/BLVRA/CS/FKBP1A/RAB31/CHP1/CREG1/PLAUR/DENND5A/ACSL1/TRIB1/RAB20/RTN3/CAPN2/CD63/NOTCH2/SERINC5/CRISPLD2/TBXAS1/BEST1/PXN/ACTN1/PICALM/SELPLG/SLCO3A1/CTSB/PTAFR/DAPK1/FBP1/COTL1
## Count
## GSE5542_UNTREATED_VS_IFNA_TREATED_EPITHELIAL_CELLS_24H_UP 44
## GSE25088_ROSIGLITAZONE_VS_IL4_AND_ROSIGLITAZONE_STIM_STAT6_KO_MACROPHAGE_DAY10_UP 42
## GSE3982_EOSINOPHIL_VS_CENT_MEMORY_CD4_TCELL_UP 42
## GSE15271_CXCR4_POS_VS_NEG_GC_BCELL_DN 37
## GSE13485_DAY7_VS_DAY21_YF17D_VACCINE_PBMC_UP 39
## GSE29618_BCELL_VS_MONOCYTE_DN 39em.C8 <- enricher(gene, TERM2GENE=m_C8, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 77
em.C8.ge <- setReadable(em.C8, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C8.ge)## [1] 77 9head(em.C8.ge)## ID
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB
## AIZARANI_LIVER_C20_LSECS_3 AIZARANI_LIVER_C20_LSECS_3
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET
## Description
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB
## AIZARANI_LIVER_C20_LSECS_3 AIZARANI_LIVER_C20_LSECS_3
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET
## GeneRatio
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL 53/1191
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB 36/1191
## AIZARANI_LIVER_C20_LSECS_3 50/1191
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL 47/1191
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B 25/1191
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 41/1191
## BgRatio
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL 276/18801
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB 169/18801
## AIZARANI_LIVER_C20_LSECS_3 295/18801
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL 270/18801
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B 103/18801
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 240/18801
## pvalue
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL 2.908945e-13
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB 9.244193e-11
## AIZARANI_LIVER_C20_LSECS_3 1.561487e-10
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL 2.204784e-10
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B 4.074602e-09
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 5.493455e-09
## p.adjust
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL 1.646463e-10
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB 2.616107e-08
## AIZARANI_LIVER_C20_LSECS_3 2.946006e-08
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL 3.119769e-08
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B 4.612449e-07
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 5.182159e-07
## qvalue
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL 1.331991e-10
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB 2.116434e-08
## AIZARANI_LIVER_C20_LSECS_3 2.383323e-08
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL 2.523898e-08
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B 3.731477e-07
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 4.192374e-07
## geneID
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL KIF13B/CPM/HSD17B12/RALB/STX3/ZNRF1/SMYD3/TMEM154/SWAP70/SYTL3/RHBDD2/PIK3R6/TMEM220/BLVRA/IL1RL1/EPAS1/GSTM3/CLU/SLC45A3/NENF/ALOX5AP/CD9/ARHGAP18/PHF20/FOXP1/GALC/KCNH2/NDST2/CD59/CD63/MITF/AKAP13/PRNP/TNIK/NDFIP2/TMOD1/CHN2/PARVB/PMP22/CTNNBL1/LAX1/TESPA1/SIGLEC8/ST3GAL4/IL5RA/SLC18A2/KIAA1522/ZBTB32/RAB37/TESC/CAPG/LPCAT2/ACOT7
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB LPP/TNS3/ITPR2/SVIL/KIF13B/ETV6/LRRFIP1/CPM/LINC-PINT/RALGAPA2/SDCCAG8/EXT1/SPIDR/PLEKHA7/STK3/MECOM/ARHGAP24/CAMKMT/KIAA1958/PRKCE/AFF1/MED13L/OSBPL3/FOXP1/LAMB1/DOCK1/PFKFB3/PITPNC1/PCSK6/GALNT14/NCOA7/TRAPPC9/SASH1/TBC1D5/MSI2/MGLL
## AIZARANI_LIVER_C20_LSECS_3 DAAM1/SLC25A37/NID1/SPARC/APP/ANKRD11/TMEM51/ITPKC/ARHGEF7/COL4A1/ZEB2/CDC42BPB/FNDC3B/BAZ1A/ARSG/IL1RL1/AKAP12/TINAGL1/EPAS1/PTPN1/HERC1/FKBP1A/ASAP1/PLAUR/CD9/PLXNA2/NOTCH4/ARHGAP26/NOLC1/NDRG1/CD59/EFNB2/SSH1/PRICKLE2/SLC7A1/IFI27/ERG/LDB2/PXN/ACTN1/NCOA7/PDLIM1/SASH1/SOGA1/GRB10/ACP5/HIPK2/CDK17/ENG/SNX9
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL CUX1/SLC7A7/TPP1/TGFBI/HIPK3/TNFRSF1B/FCN1/UBXN11/GNAQ/SERF2/BACH1/ZEB2/SCPEP1/RASSF2/CD4/RAB31/CHST15/KCNE3/AHNAK/ACSL1/PRKAG2/PTPRE/HCK/SPI1/NACC2/RTN3/GAS7/TET3/EFHD2/CEBPB/RASSF3/NFAM1/NOTCH2/CRISPLD2/TKT/DICER1/RNF144B/USP15/CCNY/ENTPD1/SULF2/PICALM/NADK/HK2/CARS2/MAP3K1/COTL1
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B LPP/CELF2/KIF13B/RALGAPA2/SDCCAG8/WWOX/HERC1/PRKCE/KMT2C/ARHGAP18/DGKI/SEMA3C/OSBPL3/ARL15/FOXP1/MITF/CLNK/NEDD4L/NCOA7/PICALM/PTPRJ/TBC1D5/MSI2/MYRIP/GPHN
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET SSH2/KIF13B/GPX3/LRRFIP1/LINC-PINT/TMEM51/EXT1/STAT3/SMYD3/MECOM/BACH1/UBE2D3/AAK1/HERC1/CSGALNACT1/PRKCE/ERC1/AFF1/MED13L/ABTB2/SH3RF1/AGBL4/IFRD1/AHNAK/SREBF2/PRKAG2/OSBPL3/ARID1B/ARL15/ACTN4/LAMB1/RBPMS/PFKFB3/DYRK1A/NDRG1/MCU/NEDD4L/NCOA7/SPTBN1/SLC25A25/MAP3K14
## Count
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL 53
## LAKE_ADULT_KIDNEY_C11_THIN_ASCENDING_LIMB 36
## AIZARANI_LIVER_C20_LSECS_3 50
## TRAVAGLINI_LUNG_CLASSICAL_MONOCYTE_CELL 47
## LAKE_ADULT_KIDNEY_C21_COLLECTING_DUCT_INTERCALATED_CELLS_TYPE_B 25
## LAKE_ADULT_KIDNEY_C17_COLLECTING_SYSTEM_PCS_STRESSED_DISSOC_SUBSET 41 # no gene set enrichment here using GSEA
em.H.gsea <- GSEA(geneList.na, TERM2GENE = m_H)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...em.C2.gsea <- GSEA(geneList.na, TERM2GENE = m_C2)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...em.C3.gsea <- GSEA(geneList.na, TERM2GENE = m_C3)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...em.C5.gsea <- GSEA(geneList.na, TERM2GENE = m_C5)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...em.C7.gsea <- GSEA(geneList.na, TERM2GENE = m_C7)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...em.C8.gsea <- GSEA(geneList.na, TERM2GENE = m_C8)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...# Biological theme comparison
# to calculate enriched functional categories of each gene clusters
# Visualization of profile comparison
mydf <- data.frame(Entrez=names(geneList), FC=geneList)
colnames(mydf)[2] <- c("coeff")
mydf <- mydf[abs(mydf$coeff) > 0,]
mydf$Group <- "Hypermethylated"
mydf$Group[mydf$coeff < 0] <- "Hypomethylated"
table(mydf$Group)##
## Hypermethylated Hypomethylated
## 190 1319mydf$Group <- as.factor(mydf$Group)
formula_res <- compareCluster(Entrez~Group, data=mydf, fun="enrichKEGG") # 10
formula_res.ge <- setReadable(formula_res, 'org.Hs.eg.db', 'ENTREZID')
head(formula_res.ge)## Cluster Group ID
## 1 Hypomethylated Hypomethylated hsa04070
## 2 Hypomethylated Hypomethylated hsa00512
## 3 Hypomethylated Hypomethylated hsa04921
## 4 Hypomethylated Hypomethylated hsa05167
## 5 Hypomethylated Hypomethylated hsa04371
## 6 Hypomethylated Hypomethylated hsa04725
## Description GeneRatio BgRatio
## 1 Phosphatidylinositol signaling system 21/555 97/8113
## 2 Mucin type O-glycan biosynthesis 10/555 36/8113
## 3 Oxytocin signaling pathway 24/555 154/8113
## 4 Kaposi sarcoma-associated herpesvirus infection 27/555 194/8113
## 5 Apelin signaling pathway 21/555 139/8113
## 6 Cholinergic synapse 18/555 113/8113
## pvalue p.adjust qvalue
## 1 1.729020e-06 0.0005515573 0.0004313449
## 2 1.035595e-04 0.0120653439 0.0094356921
## 3 1.134672e-04 0.0120653439 0.0094356921
## 4 3.013938e-04 0.0240361524 0.0187974530
## 5 4.616639e-04 0.0294541565 0.0230345986
## 6 6.087850e-04 0.0323670716 0.0253126414
## geneID
## 1 ITPKC/CALML4/PTEN/PI4KA/INPP5F/PIP4K2A/PIP5K1B/PRKCB/PI4KB/PIK3CB/DGKI/IP6K2/ITPK1/INPP5A/CALM1/DGKG/PIK3R1/ITPKB/INPP4A/ITPR1/MTMR3
## 2 ST3GAL2/GALNT7/GALNTL6/GALNT12/GALNT10/GALNT16/ST6GALNAC4/GALNT14/ST3GAL1/GALNT6
## 3 CALML4/GNAQ/MYLK4/PIK3R6/KCNJ6/MAP2K5/CACNA2D1/PRKCB/CACNA1S/NFATC2/PRKAG2/CAMK1D/SRC/CACNA1D/MYLK/PRKAB1/PIK3R5/MYL9/CALM1/EEF2K/GNAO1/CAMK2G/ITPR1/MYLK3
## 4 CALML4/STAT1/STAT3/GNG7/TRAF3/PIK3R6/CDK6/MAPK13/ATG14/PIK3CB/GNG12/NFATC2/PREX1/HCK/SRC/TCF7/GNB5/ANGPT2/RB1/PIK3R5/CALM1/MAP1LC3B2/FADD/PIK3R1/CREBBP/ITPR1/LEF1
## 5 CALML4/GNG7/GNAQ/MYLK4/PIK3R6/PRKCE/GNG12/PRKAG2/MYLK/PRKAB1/GNB5/PIK3R5/JAG1/CALM1/MAP1LC3B2/MEF2D/HDAC4/SPHK2/ITPR1/CDH1/MYLK3
## 6 GNG7/GNAQ/CREB3L2/PIK3R6/KCNJ6/CHRM1/PRKCB/CACNA1S/PIK3CB/GNG12/CACNA1D/GNB5/PIK3R5/PIK3R1/FYN/GNAO1/CAMK2G/ITPR1
## Count
## 1 21
## 2 10
## 3 24
## 4 27
## 5 21
## 6 18save(formula_res.ge, file=file.path(res.dir,
paste0("compareCluster_enrichKEGG_CRA_CAMP_", timeStamp, ".RData")))
write.table(formula_res.ge,file=file.path(res.dir,
paste0("compareCluster_enrichKEGG_CRA_CAMP_",timeStamp,".txt"))
,sep="\t",row.names=F,quote=F)
enrichplot::dotplot(formula_res.ge, x=~Group, showCategory=10)
pdf(file = file.path(sub.plots.dir, "dotplot_theme_cluster_hypo_enrichKEGG_CRA_CAMP.pdf"),
width = 7, height = 7)
enrichplot::dotplot(formula_res.ge, x=~Group, showCategory=10)
dev.off()## png
## 2# Enrichment map organizes enriched terms into a network with edges connecting overlapping gene sets. In this way, mutually overlapping gene sets are tend to cluster together, making it easy to identify functional module
x2 <- pairwise_termsim(formula_res.ge)
emapplot(x2)
# if you don't want to plot effect sizes
#p1 <- cnetplot(edox, node_label="category")
#p2 <- cnetplot(edox, node_label="gene")
#p3 <- cnetplot(edox, node_label="all")
#p4 <- cnetplot(edox, node_label="none") 6. clusterProfileR enrichment analysis for CRA, CAMP and FHS
coeff.cra <- merge_CG.all$beta_coeff_cra
names(coeff.cra) <- merge_CG.all$Gene.x
coeff.cra.df <- data.frame(coeff.cra)
coeff.cra.df$Gene <- names(coeff.cra)
coeff.cra.uniq <- coeff.cra.df$Gene[!is.na(coeff.cra.df$Gene)]
coeff.cra.uniq <- coeff.cra.df[!is.na(coeff.cra.df$Gene), ]
coeff.cra.uniq <- coeff.cra.df[coeff.cra.df$Gene!="NA",]
coeff.cra.uniq <- coeff.cra.df[!duplicated(coeff.cra.df$Gene), ]
coeff.cra.uniq.v <- coeff.cra.uniq$coeff.cra
names(coeff.cra.uniq.v) <- coeff.cra.uniq$Gene
geneList <- coeff.cra.uniq.v
geneList <- sort(geneList, decreasing = TRUE)
entrezid <- names(geneList)
symbols.entrez <- mapIds(org.Hs.eg.db, entrezid, 'ENTREZID', 'SYMBOL')## 'select()' returned 1:1 mapping between keys and columnslength(symbols.entrez) # 145## [1] 145#ids <- as.numeric(symbols.entrez)
length(unique(symbols.entrez)) # 126## [1] 126ids <- lapply(symbols.entrez, as.numeric)
#ids <- as.numeric(symbols.entrez)
names(geneList) <- ids
gene <- names(geneList)
# this looks interesting
edo.dgn <- enrichDGN(gene, pvalueCutoff = 0.05,pAdjustMethod = "BH",qvalueCutoff = 0.05)
barplot(edo.dgn, showCategory=20)
edo.dgn.ge <- setReadable(edo.dgn, 'org.Hs.eg.db', 'ENTREZID')
head(edo.dgn.ge)## ID Description GeneRatio BgRatio
## C0861155 C0861155 Rhinoconjunctivitis 4/122 14/21671
## C0038273 C0038273 Stereotypic Movement Disorder 8/122 192/21671
## C0340076 C0340076 Asthmatic pulmonary eosinophilia 5/122 62/21671
## C0034068 C0034068 Pulmonary Eosinophilia 5/122 70/21671
## C0155877 C0155877 Allergic asthma 10/122 371/21671
## C0035372 C0035372 Rett Syndrome 8/122 234/21671
## pvalue p.adjust qvalue
## C0861155 9.161390e-07 0.002841863 0.002411856
## C0038273 1.334676e-05 0.020700821 0.017568548
## C0340076 2.607175e-05 0.026958192 0.022879107
## C0034068 4.704474e-05 0.027615159 0.023436667
## C0155877 4.825106e-05 0.027615159 0.023436667
## C0035372 5.485541e-05 0.027615159 0.023436667
## geneID Count
## C0861155 IL13/IL4/IL5RA/NR0B2 4
## C0038273 EZR/SYNGAP1/IL13/TNIK/CREBBP/MITF/RERE/TRAPPC9 8
## C0340076 IL13/SIGLEC8/IL4/IL5RA/EPX 5
## C0034068 IL13/SIGLEC8/IL4/IL5RA/EPX 5
## C0155877 EZR/MCC/IL13/SIGLEC8/IL4/IL5RA/INPP4A/EPX/SLC25A25/ZFPM1 10
## C0035372 IGF1R/RHOBTB2/IL13/NCOR2/CREBBP/IL4/LBR/FBP1 8# can be saved later depending on which view we choose
cnetplot(edo.dgn.ge, categorySize="qvalue", foldChange=geneList)
# without fold change but shows enriched terms, description and annotated genes, showCategory:number of enriched terms to display
cnetplot(edo.dgn.ge, node_label="all", categorySize="qvalue")
enrichplot::dotplot(edo.dgn.ge, showCategory=20) + ggtitle("dotplot for DO")## wrong orderBy parameter; set to default `orderBy = "x"`
save(edo.dgn.ge, file=file.path(res.dir,
paste0("enrich_DGN_CRA_CAMP_FHS_", timeStamp, ".RData")))
write.table(edo.dgn.ge@result,file=file.path(res.dir,
paste0("enrichDGN_CRA_CAMP_FHS_",timeStamp,".txt"))
,sep="\t",row.names=F,quote=F)
pdf(file = file.path(sub.plots.dir, "barplot_enrichDGN_CRA_CAMP_FHS.pdf"),width = 7, height = 7)
barplot(edo.dgn.ge, showCategory=20)
dev.off()## png
## 2pdf(file = file.path(sub.plots.dir, "dotplot_enrichDGN_CRA_CAMP_FHS.pdf"),width = 7, height = 7)
enrichplot::dotplot(edo.dgn.ge, showCategory=20) + ggtitle("dotplot for DO")## wrong orderBy parameter; set to default `orderBy = "x"`dev.off()## png
## 2# no gene sets enriched here for diseases using DysGeNET
gse.dgn <- gseDGN(geneList,
minGSSize = 10,
maxGSSize = 500,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
verbose = TRUE)## preparing geneSet collections...## GSEA analysis...## Warning in preparePathwaysAndStats(pathways, stats, minSize, maxSize,
## gseaParam, : There are duplicate gene names, fgsea may produce unexpected
## results.## no term enriched under specific pvalueCutoff...#dgn <- setReadable(dgn, 'org.Hs.eg.db')
#head(dgn, 3)
#enrichplot::dotplot(gse.dgn, showCategory=30) + ggtitle("dotplot for DO")
# Enrichment map organizes enriched terms into a network with edges connecting overlapping gene sets. In this way, mutually overlapping gene sets are tend to cluster together, making it easy to identify functional module
x <- pairwise_termsim(edo.dgn.ge)
emapplot(x)
pdf(file = file.path(sub.plots.dir, "enrichmentMap_pairwise_gseDGN_CRA_CAMP_FHS_overlap_genes.pdf"),
width = 11, height = 9)
emapplot(x)
dev.off()## png
## 2# nothing
enr.do <- enrichDO(gene = gene,
ont = "DO",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe = univ,
minGSSize = 10,
maxGSSize = 500,
qvalueCutoff = 0.05,
readable = FALSE)
dim(enr.do) # nothing## [1] 0 9head(enr.do)## [1] ID Description GeneRatio BgRatio pvalue p.adjust
## [7] qvalue geneID Count
## <0 rows> (or 0-length row.names)gene.df <- bitr(gene, fromType = "ENTREZID",
toType = c("ENSEMBL", "SYMBOL"),
OrgDb = org.Hs.eg.db)## 'select()' returned 1:many mapping between keys and columns## Warning in bitr(gene, fromType = "ENTREZID", toType = c("ENSEMBL", "SYMBOL"), :
## 1.59% of input gene IDs are fail to map...head(gene.df)## ENTREZID ENSEMBL SYMBOL
## 1 3678 ENSG00000161638 ITGA5
## 3 9637 ENSG00000171055 FEZ2
## 4 2683 ENSG00000086062 B4GALT1
## 5 322 ENSG00000166313 APBB1
## 6 863 ENSG00000129993 CBFA2T3
## 7 23648 ENSG00000157216 SSBP3# just returns functional profile of a geneset at a specific GO level not a P-value
ggo <- groupGO(gene = gene,
OrgDb = org.Hs.eg.db,
ont = "BP",
level = 2,
readable = TRUE)
dim(ggo)## [1] 31 5head(ggo)## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/126
## GO:0002376 GO:0002376 immune system process 34 34/126
## GO:0006791 GO:0006791 sulfur utilization 0 0/126
## GO:0006794 GO:0006794 phosphorus utilization 0 0/126
## GO:0007610 GO:0007610 behavior 6 6/126
## GO:0008152 GO:0008152 metabolic process 92 92/126
## geneID
## GO:0000003 ITGA5/B4GALT1/NCOR2/SLC2A8/SLC19A1/FBXW8/MND1/CTSB
## GO:0002376 ITGA5/B4GALT1/CBFA2T3/SSBP3/IGF1R/BANK1/PRKCH/EZR/SLC7A11/DOCK1/IL13/RASSF2/CAB39/HDAC1/SPI1/EVL/CREBBP/MITF/IL4/LBR/ELMO2/PRKCZ/SLC7A1/IL5RA/PRG2/EPX/TOLLIP/MFHAS1/TTC7A/GUSB/CTSB/DAPK2/MAD1L1/ZFPM1
## GO:0006791
## GO:0006794
## GO:0007610 ITGA5/SYNGAP1/SLC7A11/PAK6/PRKCZ/GPR176
## GO:0008152 ITGA5/FEZ2/B4GALT1/APBB1/CBFA2T3/SSBP3/IGF1R/AXIN1/COL15A1/A2ML1/ELL2/ACOT7/UBE2QL1/SIK2/NDUFS6/MICAL2/BANK1/PRKCH/EZR/LTBP4/SYNGAP1/SLC7A11/UBE3B/IL13/RASSF2/KSR1/AGPAT1/NCOR2/PAK6/B4GALT7/CAB39/TFF1/SLC2A8/HDAC1/NOLC1/TMEM86B/SPI1/CLK3/CPSF4L/MCM2/SLC17A4/ST3GAL1/NHLRC4/ZNF862/ZNF662/ARID3A/USP20/TNIK/CREBBP/SLC19A1/MITF/DAP/IL4/LBR/NFIA/MECR/TRERF1/PNPLA1/PRKCZ/NDOR1/SEC16B/RERE/PTPRS/IL5RA/INPP4A/NR0B2/EPX/TOLLIP/PCYT1A/LPIN1/AQP1/GUCA2A/MFHAS1/TTC7A/NDFIP2/SLC25A25/FBP1/LPCAT3/FBXW8/GUSB/LRSAM1/MND1/TRAPPC9/ENG/LPCAT2/ACP5/CTSB/EZH2/SAMD11/MIR202/DAPK2/ZFPM1# nothing came up here surprisingly for BP so chose ALL: BP, CC and MF
ego <- enrichGO(gene = gene,
OrgDb = org.Hs.eg.db,
ont = "ALL",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
readable = TRUE)
dim(ego) # 8## [1] 8 10save(ego, file=file.path(res.dir,
paste0("enrich_GO_CRA_CAMP_FHS_all_overlap_results_", timeStamp, ".RData")))
write.table(ego@result,file=file.path(res.dir,
paste0("enrichGO_CRA_CAMP_FHS_all_overlap_results_",timeStamp,".txt"))
,sep="\t",row.names=F,quote=F)
head(ego@result, n=8)## ONTOLOGY ID Description
## GO:0045177 CC GO:0045177 apical part of cell
## GO:0016324 CC GO:0016324 apical plasma membrane
## GO:0031526 CC GO:0031526 brush border membrane
## GO:0005903 CC GO:0005903 brush border
## GO:0001085 MF GO:0001085 RNA polymerase II transcription factor binding
## GO:0003714 MF GO:0003714 transcription corepressor activity
## GO:0004674 MF GO:0004674 protein serine/threonine kinase activity
## GO:0071617 MF GO:0071617 lysophospholipid acyltransferase activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0045177 10/115 433/19559 2.398922e-04 0.0268484867 0.0253711776
## GO:0016324 9/115 361/19559 2.838068e-04 0.0268484867 0.0253711776
## GO:0031526 4/115 58/19559 3.766855e-04 0.0268484867 0.0253711776
## GO:0005903 5/115 106/19559 4.067953e-04 0.0268484867 0.0253711776
## GO:0001085 6/119 56/18352 1.631659e-06 0.0006379785 0.0005736568
## GO:0003714 8/119 194/18352 3.888987e-05 0.0076029688 0.0068364291
## GO:0004674 11/119 435/18352 1.240552e-04 0.0161685331 0.0145384037
## GO:0071617 3/119 19/18352 2.387827e-04 0.0233410120 0.0209877454
## geneID Count
## GO:0045177 AJAP1/EZR/SLC7A11/SLC17A4/TNIK/SLC19A1/PRKCZ/SLC7A1/AQP1/CTSB 10
## GO:0016324 AJAP1/EZR/SLC17A4/TNIK/SLC19A1/PRKCZ/SLC7A1/AQP1/CTSB 9
## GO:0031526 B4GALT1/SLC7A11/SLC19A1/AQP1 4
## GO:0005903 B4GALT1/EZR/SLC7A11/SLC19A1/AQP1 5
## GO:0001085 HDAC1/SPI1/CREBBP/RERE/FBP1/ZFPM1 6
## GO:0003714 CBFA2T3/NCOR2/HDAC1/CREBBP/TRERF1/RERE/NR0B2/EZH2 8
## GO:0004674 SIK2/PRKCH/LTBP4/KSR1/PAK6/CAB39/CLK3/TNIK/PRKCZ/ENG/DAPK2 11
## GO:0071617 AGPAT1/LPCAT3/LPCAT2 3barplot(ego, showCategory=20)
enrichplot::dotplot(ego, showCategory=30) + ggtitle("dotplot for ORA")## wrong orderBy parameter; set to default `orderBy = "x"`
# based on 1509 genes and 1390 unique genes
pdf(file = file.path(sub.plots.dir, "barplot_GOALL_CRA_CAMP_FHS_overlap_genes.pdf"),
width = 7, height = 7)
barplot(ego, showCategory=20)
dev.off()## png
## 2pdf(file = file.path(sub.plots.dir, "dotplot_GOALL_CRA_CAMP_FHS_overlap_genes.pdf"),
width = 7, height = 7)
enrichplot::dotplot(ego, showCategory=30) + ggtitle("dotplot for ORA")## wrong orderBy parameter; set to default `orderBy = "x"`dev.off()## png
## 2# not needed as readable=TRUE in enrichGO function
#egox <- setReadable(ego, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(ego, categorySize="qvalue", foldChange=geneList)
p1 <- cnetplot(ego, categorySize="qvalue", foldChange=geneList)
# for CAMP
coeff.camp <- merge_CG.all$logFC
names(coeff.camp) <- merge_CG.all$Gene.x
coeff.camp.df <- data.frame(coeff.camp)
coeff.camp.df$Gene <- names(coeff.camp)
coeff.camp.uniq <- coeff.camp.df$Gene[!is.na(coeff.camp.df$Gene)]
coeff.camp.uniq <- coeff.camp.df[!is.na(coeff.camp.df$Gene), ]
coeff.camp.uniq <- coeff.camp.df[coeff.camp.df$Gene!="NA",]
coeff.camp.uniq <- coeff.camp.df[!duplicated(coeff.camp.df$Gene), ]
coeff.camp.uniq.v <- coeff.camp.uniq$coeff.camp
names(coeff.camp.uniq.v) <- coeff.camp.uniq$Gene
geneList <- coeff.camp.uniq.v
geneList <- sort(geneList, decreasing = TRUE)
entrezid <- names(geneList)
symbols.entrez <- mapIds(org.Hs.eg.db, entrezid, 'ENTREZID', 'SYMBOL')## 'select()' returned 1:1 mapping between keys and columnslength(symbols.entrez) # 145## [1] 145#ids <- as.numeric(symbols.entrez)
length(unique(symbols.entrez)) # 126## [1] 126ids <- lapply(symbols.entrez, as.numeric)
#ids <- as.numeric(symbols.entrez)
names(geneList) <- ids
gene <- names(geneList)
ego <- enrichGO(gene = gene,
OrgDb = org.Hs.eg.db,
ont = "ALL",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
readable = TRUE)
# would be same outcome as for CRA as the gene list is same, just the effect estimates would change if we plot those
dim(ego)## [1] 8 10head(ego@result)## ONTOLOGY ID Description
## GO:0045177 CC GO:0045177 apical part of cell
## GO:0016324 CC GO:0016324 apical plasma membrane
## GO:0031526 CC GO:0031526 brush border membrane
## GO:0005903 CC GO:0005903 brush border
## GO:0001085 MF GO:0001085 RNA polymerase II transcription factor binding
## GO:0003714 MF GO:0003714 transcription corepressor activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0045177 10/115 433/19559 2.398922e-04 0.0268484867 0.0253711776
## GO:0016324 9/115 361/19559 2.838068e-04 0.0268484867 0.0253711776
## GO:0031526 4/115 58/19559 3.766855e-04 0.0268484867 0.0253711776
## GO:0005903 5/115 106/19559 4.067953e-04 0.0268484867 0.0253711776
## GO:0001085 6/119 56/18352 1.631659e-06 0.0006379785 0.0005736568
## GO:0003714 8/119 194/18352 3.888987e-05 0.0076029688 0.0068364291
## geneID Count
## GO:0045177 EZR/SLC7A11/AJAP1/SLC17A4/SLC7A1/TNIK/PRKCZ/SLC19A1/AQP1/CTSB 10
## GO:0016324 EZR/AJAP1/SLC17A4/SLC7A1/TNIK/PRKCZ/SLC19A1/AQP1/CTSB 9
## GO:0031526 B4GALT1/SLC7A11/SLC19A1/AQP1 4
## GO:0005903 B4GALT1/EZR/SLC7A11/SLC19A1/AQP1 5
## GO:0001085 SPI1/HDAC1/CREBBP/RERE/FBP1/ZFPM1 6
## GO:0003714 CBFA2T3/NCOR2/HDAC1/TRERF1/CREBBP/RERE/EZH2/NR0B2 8barplot(ego, showCategory=20)
#dotplot(ego)
enrichplot::dotplot(ego, showCategory=30) + ggtitle("dotplot for ORA")## wrong orderBy parameter; set to default `orderBy = "x"`
#gseaplot(y, y[1,1], title=y[1,2])
# not needed here as readable was TRUE in the enrichGO function
#egox <- setReadable(ego, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(ego, categorySize="qvalue", foldChange=geneList)
p2 <- cnetplot(ego, categorySize="qvalue", foldChange=geneList)
# only with CRA (a) and CAMP (b); for better visualizing chose nrow=2
cowplot::plot_grid(p1, p2, ncol=1,nrow=2, labels=LETTERS[1:2], rel_widths=c(.8, .8))
# For FHS
coeff.fhs <- merge_CG.all$IgE.Estimate
names(coeff.fhs) <- merge_CG.all$Gene.x
coeff.fhs.df <- data.frame(coeff.fhs)
coeff.fhs.df$Gene <- names(coeff.fhs)
coeff.fhs.uniq <- coeff.fhs.df$Gene[!is.na(coeff.fhs.df$Gene)]
coeff.fhs.uniq <- coeff.fhs.df[!is.na(coeff.fhs.df$Gene), ]
coeff.fhs.uniq <- coeff.fhs.df[coeff.fhs.df$Gene!="NA",]
coeff.fhs.uniq <- coeff.fhs.df[!duplicated(coeff.fhs.df$Gene), ]
coeff.fhs.uniq.v <- coeff.fhs.uniq$coeff.fhs
names(coeff.fhs.uniq.v) <- coeff.fhs.uniq$Gene
geneList <- coeff.fhs.uniq.v
geneList <- sort(geneList, decreasing = TRUE)
entrezid <- names(geneList)
symbols.entrez <- mapIds(org.Hs.eg.db, entrezid, 'ENTREZID', 'SYMBOL')## 'select()' returned 1:1 mapping between keys and columnslength(symbols.entrez) # 145## [1] 145#ids <- as.numeric(symbols.entrez)
length(unique(symbols.entrez)) # 126## [1] 126ids <- lapply(symbols.entrez, as.numeric)
#ids <- as.numeric(symbols.entrez)
names(geneList) <- ids
gene <- names(geneList)
ego <- enrichGO(gene = gene,
OrgDb = org.Hs.eg.db,
ont = "ALL",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
readable = TRUE)
dim(ego)## [1] 8 10head(ego@result)## ONTOLOGY ID Description
## GO:0045177 CC GO:0045177 apical part of cell
## GO:0016324 CC GO:0016324 apical plasma membrane
## GO:0031526 CC GO:0031526 brush border membrane
## GO:0005903 CC GO:0005903 brush border
## GO:0001085 MF GO:0001085 RNA polymerase II transcription factor binding
## GO:0003714 MF GO:0003714 transcription corepressor activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0045177 10/115 433/19559 2.398922e-04 0.0268484867 0.0253711776
## GO:0016324 9/115 361/19559 2.838068e-04 0.0268484867 0.0253711776
## GO:0031526 4/115 58/19559 3.766855e-04 0.0268484867 0.0253711776
## GO:0005903 5/115 106/19559 4.067953e-04 0.0268484867 0.0253711776
## GO:0001085 6/119 56/18352 1.631659e-06 0.0006379785 0.0005736568
## GO:0003714 8/119 194/18352 3.888987e-05 0.0076029688 0.0068364291
## geneID Count
## GO:0045177 AQP1/SLC19A1/EZR/SLC17A4/AJAP1/CTSB/TNIK/SLC7A11/PRKCZ/SLC7A1 10
## GO:0016324 AQP1/SLC19A1/EZR/SLC17A4/AJAP1/CTSB/TNIK/PRKCZ/SLC7A1 9
## GO:0031526 B4GALT1/AQP1/SLC19A1/SLC7A11 4
## GO:0005903 B4GALT1/AQP1/SLC19A1/EZR/SLC7A11 5
## GO:0001085 SPI1/CREBBP/HDAC1/RERE/FBP1/ZFPM1 6
## GO:0003714 CBFA2T3/NCOR2/CREBBP/HDAC1/RERE/EZH2/NR0B2/TRERF1 8barplot(ego, showCategory=20)
#dotplot(ego)
enrichplot::dotplot(ego, showCategory=30) + ggtitle("dotplot for ORA")## wrong orderBy parameter; set to default `orderBy = "x"`
#gseaplot(y, y[1,1], title=y[1,2])
#egox <- setReadable(ego, 'org.Hs.eg.db', 'ENTREZID')
cnetplot(ego, categorySize="qvalue", foldChange=geneList)
p3 <- cnetplot(ego, categorySize="qvalue", foldChange=geneList)
pdf(file = file.path(sub.plots.dir, "clusterProfiler_enrichGO_CRA_CAMP_coeff_overlap_with_FHS_univ.pdf"),
width = 22, height = 9)
# Genes and gene ontology enrichments network
cowplot::plot_grid(p1, p2,ncol=2, labels=LETTERS[1:2], rel_widths=c(.8, .8))
dev.off()## png
## 2# for ease in visualizing
cowplot::plot_grid(p1, p2, p3, ncol=1, nrow=3, labels=LETTERS[1:3], rel_widths=c(.8, .8,.8))
pdf(file = file.path(sub.plots.dir, "clusterProfiler_enrichGO_CRA_CAMP_FHS_coeff_overlap_univ.pdf"),
width = 35, height = 9)
# Genes and gene ontology enrichments network
cowplot::plot_grid(p1, p2, p3, ncol=3, nrow=1, labels=LETTERS[1:3], rel_widths=c(.8, .8,.8))
dev.off()## png
## 2# If you don't want effect estimates
cnetplot(ego, categorySize="qvalue", node_label="all")
# save it
pdf(file = file.path(sub.plots.dir, "clusterProfiler_enrichGO_CRA_CAMP_FHS_overlap_without_coeff.pdf"),
width = 11, height = 9)
cnetplot(ego, categorySize="qvalue", node_label="all")
dev.off()## png
## 2# Enrichment map organizes enriched terms into a network with edges connecting overlapping gene sets. In this way, mutually overlapping gene sets are tend to cluster together, making it easy to identify functional module
# The plot would look same for CRA, CAMP and FHS as you are only plotting pvalues and terms
x1 <- pairwise_termsim(ego)
emapplot(x1)
pdf(file = file.path(sub.plots.dir, "enrichmentMap_pairwise_enrichGO_CRA_CAMP_FHS_overlap_genes.pdf"),
width = 11, height = 9)
emapplot(x1)
dev.off()## png
## 2kk <- enrichKEGG(gene = gene,
organism = 'hsa',
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
qvalueCutoff = 0.05,
minGSSize = 50,
maxGSSize = 500)
dim(kk) # nothing## [1] 0 9kk.ge <- setReadable(kk, 'org.Hs.eg.db', 'ENTREZID')
head(kk.ge)## [1] ID Description GeneRatio BgRatio pvalue p.adjust
## [7] qvalue geneID Count
## <0 rows> (or 0-length row.names)#save(kk.ge, file=file.path(res.dir,
# paste0("enrich_Kegg_CRA_CAMP_FHS_genomewide_thresh_", timeStamp, #".RData")))
#write.table(kk.ge@result,file=file.path(res.dir,
# paste0("enrichKegg_CRA_CAMP_gw_thresh_",timeStamp,".txt"))
# ,sep="\t",row.names=F,quote=F)
geneList.na <- geneList[names(geneList)!="NA"]
kk2 <- gseKEGG(geneList = geneList.na,
organism = 'hsa',
minGSSize = 50,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
maxGSSize = 500,
by = "fgsea",
verbose = TRUE)## preparing geneSet collections...
## GSEA analysis...## no term enriched under specific pvalueCutoff...head(kk2)## [1] ID Description setSize enrichmentScore
## [5] NES pvalue p.adjust qvalues
## <0 rows> (or 0-length row.names)#preparing geneSet collections...
#GSEA analysis...
#no term enriched under specific pvalueCutoff...
# GSEA , no enrichment
ego.gse <- gseGO(geneList = geneList.na,
OrgDb = org.Hs.eg.db,
ont = "BP",
minGSSize = 50,
maxGSSize = 500,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
verbose = TRUE)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...dim(ego.gse)## [1] 0 8# H and C2,3,5,7,8
# Gene set enrichment analysis.. The same pulled gene sets from msigdbr could be used as above in section 4
# enrichments
em.H <- enricher(gene, TERM2GENE=m_H, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # none, nothing was sig
dim(em.H)## [1] 0 9em.C2 <- enricher(gene, TERM2GENE=m_C2, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 34
em.C2.ge <- setReadable(em.C2, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C2.ge)## [1] 34 9# top curated gene set is for KEGG asthma which was interesting
head(em.C2.ge)## ID
## KEGG_ASTHMA KEGG_ASTHMA
## SENESE_HDAC3_TARGETS_UP SENESE_HDAC3_TARGETS_UP
## PID_ERA_GENOMIC_PATHWAY PID_ERA_GENOMIC_PATHWAY
## APPEL_IMATINIB_RESPONSE APPEL_IMATINIB_RESPONSE
## PEREZ_TP63_TARGETS PEREZ_TP63_TARGETS
## WEST_ADRENOCORTICAL_TUMOR_UP WEST_ADRENOCORTICAL_TUMOR_UP
## Description GeneRatio BgRatio
## KEGG_ASTHMA KEGG_ASTHMA 4/123 30/21697
## SENESE_HDAC3_TARGETS_UP SENESE_HDAC3_TARGETS_UP 12/123 496/21697
## PID_ERA_GENOMIC_PATHWAY PID_ERA_GENOMIC_PATHWAY 5/123 64/21697
## APPEL_IMATINIB_RESPONSE APPEL_IMATINIB_RESPONSE 4/123 33/21697
## PEREZ_TP63_TARGETS PEREZ_TP63_TARGETS 10/123 360/21697
## WEST_ADRENOCORTICAL_TUMOR_UP WEST_ADRENOCORTICAL_TUMOR_UP 9/123 298/21697
## pvalue p.adjust qvalue
## KEGG_ASTHMA 2.404427e-05 0.01667970 0.01476813
## SENESE_HDAC3_TARGETS_UP 2.580739e-05 0.01667970 0.01476813
## PID_ERA_GENOMIC_PATHWAY 3.148396e-05 0.01667970 0.01476813
## APPEL_IMATINIB_RESPONSE 3.543317e-05 0.01667970 0.01476813
## PEREZ_TP63_TARGETS 3.978936e-05 0.01667970 0.01476813
## WEST_ADRENOCORTICAL_TUMOR_UP 5.164913e-05 0.01804276 0.01597498
## geneID
## KEGG_ASTHMA PRG2/IL4/IL13/EPX
## SENESE_HDAC3_TARGETS_UP B4GALT1/GPR176/UBE2QL1/EZR/MICAL2/CTSB/LPIN1/BICD2/PMP22/TNIK/SLC7A11/SLC7A1
## PID_ERA_GENOMIC_PATHWAY APBB1/NCOR2/HDAC1/TFF1/NR0B2
## APPEL_IMATINIB_RESPONSE GUSB/ENG/ACP5/CTSB
## PEREZ_TP63_TARGETS KCNH2/PAK6/UBE2QL1/METRNL/IGF1R/RAB11FIP4/PRKCH/ST3GAL1/KSR1/ZFPM1
## WEST_ADRENOCORTICAL_TUMOR_UP ELMO2/ACOT7/MCM2/HDAC1/EZH2/LPIN1/BICD2/MAD1L1/SLC7A11
## Count
## KEGG_ASTHMA 4
## SENESE_HDAC3_TARGETS_UP 12
## PID_ERA_GENOMIC_PATHWAY 5
## APPEL_IMATINIB_RESPONSE 4
## PEREZ_TP63_TARGETS 10
## WEST_ADRENOCORTICAL_TUMOR_UP 9# regulatory target/motif gene sets
em.C3 <- enricher(gene, TERM2GENE=m_C3, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 1
em.C3.ge <- setReadable(em.C3, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C3.ge)## [1] 1 9head(em.C3.ge)## ID Description GeneRatio BgRatio pvalue p.adjust
## GATA1_05 GATA1_05 GATA1_05 9/123 284/28103 4.663766e-06 0.008865819
## qvalue geneID
## GATA1_05 0.0075553 GUCA2A/PRG2/IL4/SAMD11/TMEM86B/SLC25A25/SEC16B/EPX/ZFPM1
## Count
## GATA1_05 9# ontology gene sets
em.C5 <- enricher(gene, TERM2GENE=m_C5, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 4
em.C5.ge <- setReadable(em.C5, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C5.ge)## [1] 4 9head(em.C5.ge)## ID
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY
## GOBP_GRANULOCYTE_DIFFERENTIATION GOBP_GRANULOCYTE_DIFFERENTIATION
## Description
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY
## GOBP_GRANULOCYTE_DIFFERENTIATION GOBP_GRANULOCYTE_DIFFERENTIATION
## GeneRatio BgRatio
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING 6/121 52/19303
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY 9/121 182/19303
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY 12/121 480/19303
## GOBP_GRANULOCYTE_DIFFERENTIATION 4/121 33/19303
## pvalue p.adjust
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING 8.614132e-07 0.003211349
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY 2.204261e-06 0.004108742
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY 4.909021e-05 0.048673240
## GOBP_GRANULOCYTE_DIFFERENTIATION 5.222451e-05 0.048673240
## qvalue
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING 0.002907043
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY 0.003719400
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY 0.044060992
## GOBP_GRANULOCYTE_DIFFERENTIATION 0.044060992
## geneID
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING SPI1/CREBBP/HDAC1/RERE/FBP1/ZFPM1
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY CBFA2T3/NCOR2/CREBBP/HDAC1/RERE/EZH2/NR0B2/TRERF1/ZFPM1
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY CBFA2T3/APBB1/NCOR2/CREBBP/HDAC1/RERE/EZH2/NR0B2/LPIN1/TRERF1/ARID3A/ZFPM1
## GOBP_GRANULOCYTE_DIFFERENTIATION CBFA2T3/LBR/SPI1/ZFPM1
## Count
## GOMF_RNA_POLYMERASE_II_TRANSCRIPTION_FACTOR_BINDING 6
## GOMF_TRANSCRIPTION_COREPRESSOR_ACTIVITY 9
## GOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY 12
## GOBP_GRANULOCYTE_DIFFERENTIATION 4# immunologic signature gene sets
em.C7 <- enricher(gene, TERM2GENE=m_C7, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 28
em.C7.ge <- setReadable(em.C7, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C7.ge)## [1] 28 9head(em.C7.ge)## ID
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP
## Description
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP
## GeneRatio
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN 8/123
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP 7/123
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN 7/123
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP 8/123
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP 8/123
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP 8/123
## BgRatio
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN 178/21341
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP 134/21341
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN 139/21341
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP 196/21341
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP 198/21341
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP 200/21341
## pvalue
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN 9.114129e-06
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP 1.274884e-05
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN 1.618327e-05
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP 1.834254e-05
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP 1.973432e-05
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP 2.121375e-05
## p.adjust
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN 0.01082697
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP 0.01082697
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN 0.01082697
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP 0.01082697
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP 0.01082697
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP 0.01082697
## qvalue
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN 0.009699708
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP 0.009699708
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN 0.009699708
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP 0.009699708
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP 0.009699708
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP 0.009699708
## geneID
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN MPRIP/ELMO2/SLC45A4/NCOR2/GUSB/PCYT1A/MICAL2/PRKCH
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP B4GALT1/NCOR2/NDOR1/MIR202/TMEM86B/RHOBTB2/TOMM34
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN ITGA5/LRIG1/RERE/IGF1R/EVL/MAD1L1/MFHAS1
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP LPCAT2/ENG/MICAL2/FBP1/ZNF862/ST3GAL1/IL5RA/MFHAS1
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP MPRIP/LRIG1/LPIN1/PRKCH/LTBP4/EVL/TNIK/PRKCZ
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP PTPRS/DAP/EZR/EZH2/ENG/ACP5/ST3GAL1/MFHAS1
## Count
## GSE6259_33D1_POS_VS_DEC205_POS_FLT3L_INDUCED_SPLENIC_DC_DN 8
## GSE12963_ENV_NEF_VS_ENV_NEF_AND_VPR_DEFICIENT_HIV1_INF_CD4_TCELL_UP 7
## GSE13522_CTRL_VS_T_CRUZI_Y_STRAIN_INF_SKIN_BALBC_MOUSE_DN 7
## GSE18281_MEDULLARY_THYMOCYTE_VS_WHOLE_MEDULLA_THYMUS_UP 8
## GSE22886_NAIVE_TCELL_VS_MONOCYTE_UP 8
## GOLDRATH_NAIVE_VS_MEMORY_CD8_TCELL_UP 8# cell type signature gene sets
em.C8 <- enricher(gene, TERM2GENE=m_C8, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05) # 2
em.C8.ge <- setReadable(em.C8, 'org.Hs.eg.db', 'ENTREZID')
dim(em.C8.ge)## [1] 2 9head(em.C8.ge)## ID
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2
## Description
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2
## GeneRatio BgRatio
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL 9/112 276/18801
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 5/112 97/18801
## pvalue
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL 4.084318e-05
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 2.858505e-04
## p.adjust qvalue
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL 0.01311066 0.0119950
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 0.04587901 0.0419749
## geneID
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL ACOT7/KCNH2/MITF/SIGLEC8/LPCAT2/IL5RA/PMP22/TNIK/NDFIP2
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 AQP1/TMEM86B/ACP5/NR0B2/FBP1
## Count
## TRAVAGLINI_LUNG_BASOPHIL_MAST_1_CELL 9
## GAO_SMALL_INTESTINE_24W_C4_ENTEROCYTE_PROGENITOR_SUBTYPE_2 5 # no gene set enrichment using GSEA
em.H.gsea <- GSEA(geneList.na, TERM2GENE = m_H)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...em.C2.gsea <- GSEA(geneList.na, TERM2GENE = m_C2)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...em.C3.gsea <- GSEA(geneList.na, TERM2GENE = m_C3)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...em.C5.gsea <- GSEA(geneList.na, TERM2GENE = m_C5)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...em.C7.gsea <- GSEA(geneList.na, TERM2GENE = m_C7)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...em.C8.gsea <- GSEA(geneList.na, TERM2GENE = m_C8)## preparing geneSet collections...## GSEA analysis...## no term enriched under specific pvalueCutoff...# Biological theme comparison
# to calculate enriched functional categories of each gene clusters
# Visualization of profile comparison
mydf <- data.frame(Entrez=names(geneList), FC=geneList)
colnames(mydf)[2] <- c("coeff")
mydf <- mydf[abs(mydf$coeff) > 0,]
mydf$Group <- "Hypermethylated"
mydf$Group[mydf$coeff < 0] <- "Hypomethylated"
table(mydf$Group)##
## Hypermethylated Hypomethylated
## 6 139mydf$Group <- as.factor(mydf$Group)
formula_res <- compareCluster(Entrez~Group, data=mydf, fun="enrichKEGG")
formula_res.ge <- setReadable(formula_res, 'org.Hs.eg.db', 'ENTREZID')
head(formula_res.ge)## Cluster Group ID Description GeneRatio BgRatio
## 1 Hypomethylated Hypomethylated hsa05310 Asthma 4/63 31/8113
## pvalue p.adjust qvalue geneID Count
## 1 8.877957e-05 0.01455985 0.01455985 PRG2/IL4/IL13/EPX 4enrichplot::dotplot(formula_res.ge, x=~Group, showCategory=10)
x2 <- pairwise_termsim(formula_res.ge)
#enrichplot::emapplot(x2)
# if you don't want to plot effect sizes
#p1 <- cnetplot(edox, node_label="category")
#p2 <- cnetplot(edox, node_label="gene")
#p3 <- cnetplot(edox, node_label="all")
#p4 <- cnetplot(edox, node_label="none")
save(formula_res.ge, file=file.path(res.dir,
paste0("compareCluster_enrichKEGG_CRA_CAMP_FHS_", timeStamp, ".RData")))
write.table(formula_res.ge,file=file.path(res.dir,
paste0("compareCluster_enrichKEGG_CRA_CAMP_FHS_",timeStamp,".txt"))
,sep="\t",row.names=F,quote=F)
#Test for over-representation (enrichment), small probability of # seeing an equal or bigger overlap
# Hypergeometric pvalue for the overlap of all 3 cohorts
# 193 is the total overlap between CRA, CAMP and FHS
# 10426 is the overlap of significant DM CpGs in CRA and CAMP because eventually this number is checked for overlap with FHS
# 406318 is the platform overlap between 450K of FHS and EPIC for CRA and CAMP so the background that was tested for the analysis
# 490 is the significant DM CpGs in FHS
# we discussed removing 51 sites that did not exist on both platforms
phyper(193-1, 10426, 406318-10426, 490-51, lower.tail = FALSE, log.p=F)## [1] 7.22766e-182#7.22766e-182
# reference: https://seqqc.wordpress.com/2019/07/25/how-to-use-phyper-in-r/
# phyper(Overlap-1, group2, Total-group2, group1,lower.tail= FALSE)
# also this works:
# fisher.test(matrix(c(Overlap, group2-Overlap, group1-Overlap, Total-group2-group1 +Overlap), 2, 2), alternative='greater')$p.value
# fisher.test(matrix(c(193, 10426-193, 439-193, 406318-10426-439+193), 2, 2), alternative='greater')$p.value7. Session info
print(Sys.Date())## [1] "2021-11-29"print(Sys.time())## [1] "2021-11-29 21:36:07 EST"sessionInfo()## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## Matrix products: default
## BLAS: /app/R-4.0.3@i86-rhel7.0/lib64/R/lib/libRblas.so
## LAPACK: /app/R-4.0.3@i86-rhel7.0/lib64/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid stats4 parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] pathview_1.30.1 msigdbr_7.4.1
## [3] magrittr_2.0.1 ggnewscale_0.4.5
## [5] lattice_0.20-45 gridExtra_2.3
## [7] gprofiler2_0.2.1 knitr_1.36
## [9] R.utils_2.11.0 R.oo_1.24.0
## [11] R.methodsS3_1.8.1 org.Hs.eg.db_3.12.0
## [13] AnnotationDbi_1.52.0 clusterProfiler_3.18.1
## [15] enrichplot_1.10.2 DOSE_3.16.0
## [17] QQperm_1.0.1 gplots_3.1.1
## [19] gProfileR_0.7.0 DMRcate_2.4.1
## [21] ggpubr_0.4.0 ggplot2_3.3.5
## [23] minfi_1.36.0 bumphunter_1.32.0
## [25] locfit_1.5-9.4 iterators_1.0.13
## [27] foreach_1.5.1 Biostrings_2.58.0
## [29] XVector_0.30.0 SummarizedExperiment_1.20.0
## [31] Biobase_2.50.0 MatrixGenerics_1.2.1
## [33] matrixStats_0.61.0 GenomicRanges_1.42.0
## [35] GenomeInfoDb_1.26.7 IRanges_2.24.1
## [37] S4Vectors_0.28.1 BiocGenerics_0.36.1
## [39] limma_3.46.0
##
## loaded via a namespace (and not attached):
## [1] rappdirs_0.3.3
## [2] rtracklayer_1.50.0
## [3] ragg_1.1.3
## [4] tidyr_1.1.4
## [5] bit64_4.0.5
## [6] DelayedArray_0.16.3
## [7] data.table_1.14.2
## [8] rpart_4.1-15
## [9] KEGGREST_1.30.1
## [10] RCurl_1.98-1.5
## [11] GEOquery_2.58.0
## [12] AnnotationFilter_1.14.0
## [13] generics_0.1.1
## [14] GenomicFeatures_1.42.3
## [15] preprocessCore_1.52.1
## [16] cowplot_1.1.1
## [17] RSQLite_2.2.8
## [18] shadowtext_0.0.9
## [19] bit_4.0.4
## [20] tzdb_0.2.0
## [21] xml2_1.3.2
## [22] httpuv_1.6.3
## [23] assertthat_0.2.1
## [24] viridis_0.6.2
## [25] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
## [26] xfun_0.26
## [27] hms_1.1.1
## [28] jquerylib_0.1.4
## [29] babelgene_21.4
## [30] evaluate_0.14
## [31] missMethyl_1.24.0
## [32] promises_1.2.0.1
## [33] fansi_0.5.0
## [34] scrime_1.3.5
## [35] progress_1.2.2
## [36] caTools_1.18.2
## [37] dbplyr_2.1.1
## [38] readxl_1.3.1
## [39] Rgraphviz_2.34.0
## [40] igraph_1.2.6
## [41] DBI_1.1.1
## [42] htmlwidgets_1.5.4
## [43] reshape_0.8.8
## [44] purrr_0.3.4
## [45] ellipsis_0.3.2
## [46] crosstalk_1.2.0
## [47] dplyr_1.0.7
## [48] backports_1.3.0
## [49] permute_0.9-5
## [50] annotate_1.68.0
## [51] biomaRt_2.46.3
## [52] sparseMatrixStats_1.2.1
## [53] vctrs_0.3.8
## [54] ensembldb_2.14.1
## [55] abind_1.4-5
## [56] cachem_1.0.6
## [57] withr_2.4.2
## [58] ggforce_0.3.3
## [59] Gviz_1.34.1
## [60] BSgenome_1.58.0
## [61] checkmate_2.0.0
## [62] GenomicAlignments_1.26.0
## [63] prettyunits_1.1.1
## [64] mclust_5.4.7
## [65] cluster_2.1.2
## [66] ExperimentHub_1.16.1
## [67] lazyeval_0.2.2
## [68] crayon_1.4.2
## [69] genefilter_1.72.1
## [70] labeling_0.4.2
## [71] edgeR_3.32.1
## [72] pkgconfig_2.0.3
## [73] tweenr_1.0.2
## [74] nlme_3.1-153
## [75] ProtGenerics_1.22.0
## [76] nnet_7.3-16
## [77] rlang_0.4.11
## [78] lifecycle_1.0.1
## [79] downloader_0.4
## [80] BiocFileCache_1.14.0
## [81] AnnotationHub_2.22.1
## [82] dichromat_2.0-0
## [83] polyclip_1.10-0
## [84] cellranger_1.1.0
## [85] graph_1.68.0
## [86] rngtools_1.5.2
## [87] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
## [88] base64_2.0
## [89] Matrix_1.3-4
## [90] carData_3.0-4
## [91] Rhdf5lib_1.12.1
## [92] base64enc_0.1-3
## [93] viridisLite_0.4.0
## [94] png_0.1-7
## [95] bitops_1.0-7
## [96] KernSmooth_2.23-20
## [97] rhdf5filters_1.2.1
## [98] blob_1.2.2
## [99] DelayedMatrixStats_1.12.3
## [100] doRNG_1.8.2
## [101] qvalue_2.22.0
## [102] stringr_1.4.0
## [103] nor1mix_1.3-0
## [104] readr_2.0.2
## [105] jpeg_0.1-9
## [106] rstatix_0.7.0
## [107] ggsignif_0.6.3
## [108] scales_1.1.1
## [109] memoise_2.0.0
## [110] plyr_1.8.6
## [111] zlibbioc_1.36.0
## [112] scatterpie_0.1.7
## [113] compiler_4.0.3
## [114] RColorBrewer_1.1-2
## [115] illuminaio_0.32.0
## [116] KEGGgraph_1.50.0
## [117] Rsamtools_2.6.0
## [118] DSS_2.38.0
## [119] htmlTable_2.2.1
## [120] Formula_1.2-4
## [121] MASS_7.3-54
## [122] tidyselect_1.1.1
## [123] stringi_1.7.5
## [124] forcats_0.5.1
## [125] textshaping_0.3.3
## [126] highr_0.9
## [127] yaml_2.2.1
## [128] GOSemSim_2.16.1
## [129] askpass_1.1
## [130] ggrepel_0.9.1
## [131] latticeExtra_0.6-29
## [132] sass_0.4.0
## [133] VariantAnnotation_1.36.0
## [134] fastmatch_1.1-3
## [135] tools_4.0.3
## [136] rio_0.5.27
## [137] rstudioapi_0.13
## [138] foreign_0.8-81
## [139] bsseq_1.26.0
## [140] farver_2.1.0
## [141] ggraph_2.0.5
## [142] rvcheck_0.1.8
## [143] digest_0.6.28
## [144] BiocManager_1.30.16
## [145] shiny_1.7.0
## [146] quadprog_1.5-8
## [147] Rcpp_1.0.7
## [148] car_3.0-11
## [149] siggenes_1.64.0
## [150] broom_0.7.10
## [151] BiocVersion_3.12.0
## [152] later_1.3.0
## [153] httr_1.4.2
## [154] biovizBase_1.38.0
## [155] colorspace_2.0-2
## [156] XML_3.99-0.6
## [157] splines_4.0.3
## [158] statmod_1.4.36
## [159] graphlayouts_0.7.1
## [160] multtest_2.46.0
## [161] systemfonts_1.0.2
## [162] plotly_4.10.0
## [163] xtable_1.8-4
## [164] jsonlite_1.7.2
## [165] tidygraph_1.2.0
## [166] ggfun_0.0.4
## [167] R6_2.5.1
## [168] Hmisc_4.5-0
## [169] pillar_1.6.4
## [170] htmltools_0.5.2
## [171] mime_0.12
## [172] DT_0.19
## [173] glue_1.5.0
## [174] fastmap_1.1.0
## [175] BiocParallel_1.24.1
## [176] interactiveDisplayBase_1.28.0
## [177] beanplot_1.2
## [178] codetools_0.2-18
## [179] fgsea_1.16.0
## [180] utf8_1.2.2
## [181] bslib_0.3.0
## [182] tibble_3.1.5
## [183] curl_4.3.2
## [184] gtools_3.9.2
## [185] zip_2.2.0
## [186] GO.db_3.12.1
## [187] openxlsx_4.2.4
## [188] openssl_1.4.5
## [189] survival_3.2-13
## [190] rmarkdown_2.11
## [191] munsell_0.5.0
## [192] DO.db_2.9
## [193] rhdf5_2.34.0
## [194] GenomeInfoDbData_1.2.4
## [195] HDF5Array_1.18.1
## [196] reshape2_1.4.4
## [197] haven_2.4.3
## [198] gtable_0.3.0